Starting phenix.real_space_refine
on Thu Feb  5 23:40:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k94_62187/02_2026/9k94_62187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k94_62187/02_2026/9k94_62187.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k94_62187/02_2026/9k94_62187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k94_62187/02_2026/9k94_62187.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k94_62187/02_2026/9k94_62187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k94_62187/02_2026/9k94_62187.map"
  }
  resolution = 4.04
  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=   0.001 sd=   0.032
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: 5
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    8115      2.51       5
     N    2150      2.21       5
     O    2430      1.98       5
     H    7960      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  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: 20690
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "H"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 914
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "B"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 914
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "E"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 914
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "G"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 914
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "I"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "J"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 914
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
  Time building chain proxies: 3.55, per 1000 atoms: 0.17
  Number of scatterers: 20690
  At special positions: 0
  Unit cell: (115.92, 117.76, 81.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     O    2430      8.00
     N    2150      7.00
     C    8115      6.00
     H    7960      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  97 " distance=2.50
    Simple disulfide: pdb=" SG  CYS H  24 " - pdb=" SG  CYS H  97 " distance=2.27
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  97 " distance=2.50
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.27
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  97 " distance=2.50
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  97 " distance=2.29
    Simple disulfide: pdb=" SG  CYS F  36 " - pdb=" SG  CYS F  97 " distance=2.50
    Simple disulfide: pdb=" SG  CYS G  24 " - pdb=" SG  CYS G  97 " distance=2.28
    Simple disulfide: pdb=" SG  CYS I  36 " - pdb=" SG  CYS I  97 " distance=2.51
    Simple disulfide: pdb=" SG  CYS J  24 " - pdb=" SG  CYS J  97 " distance=2.27

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 543.1 milliseconds
  

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2950

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 25 sheets defined
      8.6% alpha, 31.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 177
    Processing helix  chain 'H' and resid 30 through 34
      removed outlier: 3.687A  pdb=" N   SER H  33 " --> pdb=" O   SER H  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 177
    Processing helix  chain 'B' and resid 30 through 34
      removed outlier: 3.692A  pdb=" N   SER B  33 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'D' and resid 147 through 151
    Processing helix  chain 'D' and resid 167 through 177
    Processing helix  chain 'D' and resid 186 through 190
      removed outlier: 4.188A  pdb=" N   LEU D 190 " --> pdb=" O   TRP D 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 34
      removed outlier: 3.690A  pdb=" N   SER E  33 " --> pdb=" O   SER E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 92
    Processing helix  chain 'F' and resid 147 through 151
    Processing helix  chain 'F' and resid 167 through 177
    Processing helix  chain 'G' and resid 30 through 34
      removed outlier: 3.694A  pdb=" N   SER G  33 " --> pdb=" O   SER G  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 88 through 92
    Processing helix  chain 'I' and resid 147 through 151
    Processing helix  chain 'I' and resid 167 through 177
    Processing helix  chain 'I' and resid 186 through 190
      removed outlier: 4.167A  pdb=" N   LEU I 190 " --> pdb=" O   TRP I 187 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 30 through 34
      removed outlier: 3.693A  pdb=" N   SER J  33 " --> pdb=" O   SER J  30 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 88 through 92
    Processing sheet with id=AA1, first strand: chain 'C' and resid 119 through 120
      removed outlier: 3.867A  pdb=" N   ILE C 106 " --> pdb=" O   GLU C 101 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   THR C  34 " --> pdb=" O   MET C 161 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   MET C 161 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   CYS C  36 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   VAL C 159 " --> pdb=" O   CYS C  36 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE C 156 " --> pdb=" O   PHE C   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 133 through 135
      removed outlier: 3.931A  pdb=" N   ILE C 133 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54
      removed outlier: 6.640A  pdb=" N   ILE C  65 " --> pdb=" O   ILE C  51 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   SER C  53 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE C  63 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 9
      removed outlier: 3.627A  pdb=" N   ALA H  80 " --> pdb=" O   CYS H  24 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR H  70 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 59 through 61
      removed outlier: 6.347A  pdb=" N   LEU H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ARG H  40 " --> pdb=" O   LEU H  49 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 119 through 120
      removed outlier: 3.863A  pdb=" N   ILE A 106 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   THR A  34 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   MET A 161 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   CYS A  36 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 156 " --> pdb=" O   PHE A   9 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 135
      removed outlier: 3.930A  pdb=" N   ILE A 133 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 50 through 54
      removed outlier: 6.646A  pdb=" N   ILE A  65 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   SER A  53 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE A  63 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 9
      removed outlier: 3.649A  pdb=" N   ALA B  80 " --> pdb=" O   CYS B  24 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 59 through 61
      removed outlier: 6.173A  pdb=" N   LEU B  49 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   ARG B  40 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 119 through 120
      removed outlier: 3.867A  pdb=" N   ILE D 106 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   THR D  34 " --> pdb=" O   MET D 161 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   MET D 161 " --> pdb=" O   THR D  34 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   CYS D  36 " --> pdb=" O   VAL D 159 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL D 159 " --> pdb=" O   CYS D  36 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE D 156 " --> pdb=" O   PHE D   9 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 133 through 135
      removed outlier: 3.957A  pdb=" N   ILE D 133 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 54
      removed outlier: 6.634A  pdb=" N   ILE D  65 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  63 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ILE D  63 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 9
      removed outlier: 3.642A  pdb=" N   ALA E  80 " --> pdb=" O   CYS E  24 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 59 through 61
      removed outlier: 6.059A  pdb=" N   LEU E  49 " --> pdb=" O   ARG E  40 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ARG E  40 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 119 through 120
      removed outlier: 3.866A  pdb=" N   ILE F 106 " --> pdb=" O   GLU F 101 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   THR F  34 " --> pdb=" O   MET F 161 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   MET F 161 " --> pdb=" O   THR F  34 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   CYS F  36 " --> pdb=" O   VAL F 159 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL F 159 " --> pdb=" O   CYS F  36 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE F 156 " --> pdb=" O   PHE F   9 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 133 through 135
      removed outlier: 3.924A  pdb=" N   ILE F 133 " --> pdb=" O   LEU F  22 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 50 through 54
      removed outlier: 6.643A  pdb=" N   ILE F  65 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  63 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE F  63 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 5 through 9
      removed outlier: 3.630A  pdb=" N   ALA G  80 " --> pdb=" O   CYS G  24 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 59 through 61
      removed outlier: 6.130A  pdb=" N   LEU G  49 " --> pdb=" O   ARG G  40 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ARG G  40 " --> pdb=" O   LEU G  49 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'I' and resid 119 through 120
      removed outlier: 3.872A  pdb=" N   ILE I 106 " --> pdb=" O   GLU I 101 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR I  34 " --> pdb=" O   MET I 161 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   MET I 161 " --> pdb=" O   THR I  34 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   CYS I  36 " --> pdb=" O   VAL I 159 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   VAL I 159 " --> pdb=" O   CYS I  36 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'I' and resid 133 through 135
      removed outlier: 3.937A  pdb=" N   ILE I 133 " --> pdb=" O   LEU I  22 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'I' and resid 50 through 54
      removed outlier: 6.663A  pdb=" N   SER I  50 " --> pdb=" O   TRP I  67 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   TRP I  67 " --> pdb=" O   SER I  50 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE I  52 " --> pdb=" O   ILE I  65 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'J' and resid 5 through 9
      removed outlier: 3.638A  pdb=" N   ALA J  80 " --> pdb=" O   CYS J  24 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR J  70 " --> pdb=" O   LEU J  83 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'J' and resid 59 through 61
      removed outlier: 6.096A  pdb=" N   LEU J  49 " --> pdb=" O   ARG J  40 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   ARG J  40 " --> pdb=" O   LEU J  49 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1071 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.91

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 7960
        1.02 -     1.22: 0
        1.22 -     1.41: 5481
        1.41 -     1.61: 7519
        1.61 -     1.81: 50
  Bond restraints: 21010
  Sorted by residual:
  bond pdb=" C   ARG E  68 "
       pdb=" N   PHE E  69 "
    ideal  model  delta    sigma   weight residual
    1.328  1.444 -0.116 1.37e-02 5.33e+03 7.12e+01
  bond pdb=" C   ARG G  68 "
       pdb=" N   PHE G  69 "
    ideal  model  delta    sigma   weight residual
    1.328  1.442 -0.113 1.37e-02 5.33e+03 6.84e+01
  bond pdb=" C   GLN E  46 "
       pdb=" N   ARG E  47 "
    ideal  model  delta    sigma   weight residual
    1.330  1.433 -0.103 1.38e-02 5.25e+03 5.56e+01
  bond pdb=" C   ARG J  68 "
       pdb=" N   PHE J  69 "
    ideal  model  delta    sigma   weight residual
    1.328  1.446 -0.117 1.62e-02 3.81e+03 5.25e+01
  bond pdb=" ND2 ASN I 160 "
       pdb="HD22 ASN I 160 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.64e+01
  ... (remaining 21005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 35028
        1.68 -     3.36: 739
        3.36 -     5.05: 53
        5.05 -     6.73: 27
        6.73 -     8.41: 8
  Bond angle restraints: 35855
  Sorted by residual:
  angle pdb=" O   ARG E  68 "
        pdb=" C   ARG E  68 "
        pdb=" N   PHE E  69 "
      ideal   model   delta    sigma   weight residual
     122.09  130.50   -8.41 1.23e+00 6.61e-01 4.68e+01
  angle pdb=" O   ARG G  68 "
        pdb=" C   ARG G  68 "
        pdb=" N   PHE G  69 "
      ideal   model   delta    sigma   weight residual
     122.09  130.30   -8.21 1.23e+00 6.61e-01 4.46e+01
  angle pdb=" O   ARG J  68 "
        pdb=" C   ARG J  68 "
        pdb=" N   PHE J  69 "
      ideal   model   delta    sigma   weight residual
     122.09  130.11   -8.02 1.23e+00 6.61e-01 4.25e+01
  angle pdb=" CA  ARG E  68 "
        pdb=" C   ARG E  68 "
        pdb=" N   PHE E  69 "
      ideal   model   delta    sigma   weight residual
     118.04  109.98    8.06 1.32e+00 5.74e-01 3.73e+01
  angle pdb=" CA  ARG G  68 "
        pdb=" C   ARG G  68 "
        pdb=" N   PHE G  69 "
      ideal   model   delta    sigma   weight residual
     118.04  110.11    7.93 1.32e+00 5.74e-01 3.61e+01
  ... (remaining 35850 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 9395
       17.99 -    35.97: 779
       35.97 -    53.96: 287
       53.96 -    71.94: 47
       71.94 -    89.93: 22
  Dihedral angle restraints: 10530
    sinusoidal: 5165
      harmonic: 5365
  Sorted by residual:
  dihedral pdb=" CB  CYS I  36 "
           pdb=" SG  CYS I  36 "
           pdb=" SG  CYS I  97 "
           pdb=" CB  CYS I  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.92  -35.92     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CB  CYS D  36 "
           pdb=" SG  CYS D  36 "
           pdb=" SG  CYS D  97 "
           pdb=" CB  CYS D  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.90  -35.90     1      1.00e+01 1.00e-02 1.82e+01
  dihedral pdb=" CB  CYS F  36 "
           pdb=" SG  CYS F  36 "
           pdb=" SG  CYS F  97 "
           pdb=" CB  CYS F  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.89  -35.89     1      1.00e+01 1.00e-02 1.82e+01
  ... (remaining 10527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1338
       0.040 -    0.080: 363
       0.080 -    0.119: 206
       0.119 -    0.159: 21
       0.159 -    0.199: 2
  Chirality restraints: 1930
  Sorted by residual:
  chirality pdb=" CA  ILE I  82 "
            pdb=" N   ILE I  82 "
            pdb=" C   ILE I  82 "
            pdb=" CB  ILE I  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.90e-01
  chirality pdb=" CA  ILE F  82 "
            pdb=" N   ILE F  82 "
            pdb=" C   ILE F  82 "
            pdb=" CB  ILE F  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.24e-01
  chirality pdb=" CA  ILE I 156 "
            pdb=" N   ILE I 156 "
            pdb=" C   ILE I 156 "
            pdb=" CB  ILE I 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 1927 not shown)

  Planarity restraints: 3250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 160 "   -0.085 2.00e-02 2.50e+03   8.32e-02 1.04e+02
        pdb=" CG  ASN C 160 "    0.007 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 160 "    0.080 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 160 "    0.003 2.00e-02 2.50e+03
        pdb="HD21 ASN C 160 "    0.116 2.00e-02 2.50e+03
        pdb="HD22 ASN C 160 "   -0.120 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN F 160 "   -0.041 2.00e-02 2.50e+03   4.00e-02 2.40e+01
        pdb=" CG  ASN F 160 "    0.003 2.00e-02 2.50e+03
        pdb=" OD1 ASN F 160 "    0.038 2.00e-02 2.50e+03
        pdb=" ND2 ASN F 160 "    0.004 2.00e-02 2.50e+03
        pdb="HD21 ASN F 160 "    0.054 2.00e-02 2.50e+03
        pdb="HD22 ASN F 160 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN I 160 "   -0.027 2.00e-02 2.50e+03   2.65e-02 1.06e+01
        pdb=" CG  ASN I 160 "    0.001 2.00e-02 2.50e+03
        pdb=" OD1 ASN I 160 "    0.026 2.00e-02 2.50e+03
        pdb=" ND2 ASN I 160 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN I 160 "    0.037 2.00e-02 2.50e+03
        pdb="HD22 ASN I 160 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 3247 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 457
        2.14 -     2.75: 29422
        2.75 -     3.37: 49648
        3.37 -     3.98: 64198
        3.98 -     4.60: 96993
  Nonbonded interactions: 240718
  Sorted by model distance:
  nonbonded pdb="HG12 ILE I  82 "
            pdb="HD11 LEU I 121 "
     model   vdw
     1.521 2.440
  nonbonded pdb=" O   LEU C  83 "
            pdb="HD12 LEU C  83 "
     model   vdw
     1.656 2.620
  nonbonded pdb=" OE1 GLN I   1 "
            pdb=" H2  GLN I   1 "
     model   vdw
     1.678 2.450
  nonbonded pdb=" OE1 GLN A   1 "
            pdb=" H2  GLN A   1 "
     model   vdw
     1.682 2.450
  nonbonded pdb=" OE1 GLN F   1 "
            pdb=" H2  GLN F   1 "
     model   vdw
     1.690 2.450
  ... (remaining 240713 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:             0.100
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     17.430
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
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      :  0.011   0.475  13060  Z= 0.581
  Angle     :  0.776  17.086  17750  Z= 0.466
  Chirality :  0.046   0.199   1930
  Planarity :  0.005   0.099   2280
  Dihedral  : 14.812  89.928   4670
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 22.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 15.71 %
    Favored  : 83.93 %
  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: -2.38 (0.19), residues: 1615
  helix:  2.00 (0.62), residues: 55
  sheet: -1.09 (0.20), residues: 595
  loop : -2.20 (0.18), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  58 
 TYR   0.014   0.001   TYR D  40 
 PHE   0.010   0.001   PHE I  39 
 TRP   0.015   0.001   TRP J 113 
 HIS   0.003   0.001   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (13050)
  covalent geometry    : angle       0.70682 (17730)
  SS BOND              : bond        0.37595 (   10)
  SS BOND              : angle       9.60094 (   20)
  hydrogen bonds       : bond        0.16084 (  448)
  hydrogen bonds       : angle       6.39344 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 285
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 GLN cc_start: 0.9335 (mp10) cc_final: 0.9065 (mp10)
REVERT: C   81 GLU cc_start: 0.8910 (pt0) cc_final: 0.8637 (pt0)
REVERT: H   66 ARG cc_start: 0.8780 (tpp80) cc_final: 0.8329 (tpp80)
REVERT: A   81 GLU cc_start: 0.8907 (pt0) cc_final: 0.8607 (pt0)
REVERT: B   66 ARG cc_start: 0.8935 (tpp80) cc_final: 0.8390 (tpp80)
REVERT: B   69 PHE cc_start: 0.6973 (m-80) cc_final: 0.6689 (m-80)
REVERT: B   74 ASP cc_start: 0.7428 (t70) cc_final: 0.7197 (t0)
REVERT: B   84 MET cc_start: 0.9282 (mtm) cc_final: 0.9011 (mmm)
REVERT: B   91 ASP cc_start: 0.7756 (m-30) cc_final: 0.7503 (m-30)
REVERT: E   46 GLN cc_start: 0.8740 (mt0) cc_final: 0.8358 (pt0)
REVERT: E   66 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8287 (tpp80)
REVERT: E   84 MET cc_start: 0.9414 (mtm) cc_final: 0.9136 (mmm)
REVERT: G   25 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: G   46 GLN cc_start: 0.8674 (mt0) cc_final: 0.8203 (pt0)
REVERT: G   53 ILE cc_start: 0.9061 (tt) cc_final: 0.8781 (tp)
REVERT: G   84 MET cc_start: 0.9421 (mtm) cc_final: 0.9067 (mmm)
REVERT: G  100 ASP cc_start: 0.8112 (t0) cc_final: 0.7772 (t0)
REVERT: J   46 GLN cc_start: 0.8744 (mt0) cc_final: 0.8355 (pt0)
REVERT: J   66 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8550 (tpp80)
  outliers start: 5
  outliers final: 5
  residues processed: 290
  average time/residue: 0.1670
  time to fit residues: 72.2220
Evaluate side-chains
  251 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 246
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.0570
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.0030
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.0970
   overall best weight:    0.4108

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 ASN
C  95 HIS
H   3 HIS
H  41 GLN
** H  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  61 ASN
A  95 HIS
B   3 HIS
B  41 GLN
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 HIS
E   3 HIS
E  41 GLN
E  46 GLN
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 HIS
G   3 HIS
G  41 GLN
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  95 HIS
J   3 HIS
J  41 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.072915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2464 r_free = 0.2464 target = 0.056089 restraints weight = 80355.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2531 r_free = 0.2531 target = 0.059230 restraints weight = 33046.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.061411 restraints weight = 18203.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.062909 restraints weight = 11614.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.063943 restraints weight = 8156.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13060  Z= 0.090
  Angle     :  0.499   4.892  17750  Z= 0.264
  Chirality :  0.044   0.136   1930
  Planarity :  0.003   0.037   2280
  Dihedral  :  3.497  13.670   1780
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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: -2.01 (0.19), residues: 1615
  helix:  3.03 (0.72), residues: 55
  sheet: -0.69 (0.22), residues: 530
  loop : -2.05 (0.17), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  58 
 TYR   0.012   0.001   TYR E 112 
 PHE   0.010   0.001   PHE J  69 
 TRP   0.012   0.001   TRP E 113 
 HIS   0.006   0.001   HIS H   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (13050)
  covalent geometry    : angle       0.49816 (17730)
  SS BOND              : bond        0.00316 (   10)
  SS BOND              : angle       0.93930 (   20)
  hydrogen bonds       : bond        0.04180 (  448)
  hydrogen bonds       : angle       5.73713 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 326
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  160 ASN cc_start: 0.9308 (m-40) cc_final: 0.9106 (m-40)
REVERT: H   66 ARG cc_start: 0.9253 (tpp80) cc_final: 0.8789 (tpp80)
REVERT: H   74 ASP cc_start: 0.8344 (t0) cc_final: 0.7576 (t0)
REVERT: H  101 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.7906 (ptt180)
REVERT: B   66 ARG cc_start: 0.9314 (tpp80) cc_final: 0.8887 (tpp80)
REVERT: B   91 ASP cc_start: 0.8458 (m-30) cc_final: 0.8145 (m-30)
REVERT: B  101 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.8056 (ptt180)
REVERT: E   53 ILE cc_start: 0.9357 (tt) cc_final: 0.9138 (tp)
REVERT: E   66 ARG cc_start: 0.9287 (tpp80) cc_final: 0.8909 (tpp80)
REVERT: E   74 ASP cc_start: 0.8306 (t0) cc_final: 0.8022 (t0)
REVERT: E   84 MET cc_start: 0.9529 (mtm) cc_final: 0.9316 (mtp)
REVERT: E   91 ASP cc_start: 0.8450 (m-30) cc_final: 0.8155 (m-30)
REVERT: E  101 ARG cc_start: 0.8069 (ttt90) cc_final: 0.6927 (ptt180)
REVERT: F   81 GLU cc_start: 0.8747 (pp20) cc_final: 0.8390 (pp20)
REVERT: G   74 ASP cc_start: 0.8532 (t0) cc_final: 0.8261 (t0)
REVERT: G  101 ARG cc_start: 0.7807 (ttt90) cc_final: 0.6895 (ptt180)
REVERT: I  160 ASN cc_start: 0.9348 (m-40) cc_final: 0.9031 (m-40)
REVERT: J   53 ILE cc_start: 0.9390 (tt) cc_final: 0.9174 (tp)
REVERT: J   66 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8953 (tpp80)
REVERT: J   74 ASP cc_start: 0.7962 (t0) cc_final: 0.7438 (t0)
REVERT: J   91 ASP cc_start: 0.8690 (m-30) cc_final: 0.8379 (m-30)
REVERT: J  101 ARG cc_start: 0.7921 (ttt90) cc_final: 0.6995 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 326
  average time/residue: 0.1779
  time to fit residues: 84.3404
Evaluate side-chains
  249 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 127 optimal weight:    0.9990
   chunk 146 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 134 optimal weight:    4.9990
   chunk 117 optimal weight:   10.0000
   chunk 79 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 150 GLN
** A  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 150 GLN
B   3 HIS
D 150 GLN
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 104 HIS
** F  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 150 GLN
** G   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 150 GLN
J 104 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.067538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2355 r_free = 0.2355 target = 0.051645 restraints weight = 81886.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2419 r_free = 0.2419 target = 0.054386 restraints weight = 35802.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2462 r_free = 0.2462 target = 0.056271 restraints weight = 20311.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2493 r_free = 0.2493 target = 0.057598 restraints weight = 13335.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.058559 restraints weight = 9604.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  13060  Z= 0.198
  Angle     :  0.542   4.308  17750  Z= 0.293
  Chirality :  0.044   0.127   1930
  Planarity :  0.004   0.047   2280
  Dihedral  :  3.823  17.936   1780
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 19.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.95 (0.20), residues: 1615
  helix:  2.21 (0.67), residues: 55
  sheet: -0.64 (0.21), residues: 595
  loop : -2.02 (0.18), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  58 
 TYR   0.011   0.001   TYR H  96 
 PHE   0.022   0.001   PHE B  69 
 TRP   0.013   0.001   TRP G 113 
 HIS   0.008   0.002   HIS G   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (13050)
  covalent geometry    : angle       0.54072 (17730)
  SS BOND              : bond        0.00309 (   10)
  SS BOND              : angle       1.18399 (   20)
  hydrogen bonds       : bond        0.04508 (  448)
  hydrogen bonds       : angle       5.93738 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 ASP cc_start: 0.9270 (p0) cc_final: 0.9053 (p0)
REVERT: H   66 ARG cc_start: 0.9442 (tpp80) cc_final: 0.9103 (tpp80)
REVERT: H   74 ASP cc_start: 0.8591 (t0) cc_final: 0.8273 (t0)
REVERT: B   74 ASP cc_start: 0.8792 (t0) cc_final: 0.8177 (t0)
REVERT: B   84 MET cc_start: 0.9484 (mtm) cc_final: 0.9175 (mtm)
REVERT: B   91 ASP cc_start: 0.8594 (m-30) cc_final: 0.8318 (m-30)
REVERT: E   53 ILE cc_start: 0.9372 (tt) cc_final: 0.9156 (tp)
REVERT: E   66 ARG cc_start: 0.9494 (tpp80) cc_final: 0.9025 (tpp80)
REVERT: E   69 PHE cc_start: 0.8448 (m-10) cc_final: 0.8094 (m-10)
REVERT: E   74 ASP cc_start: 0.8604 (t0) cc_final: 0.7860 (t0)
REVERT: E   84 MET cc_start: 0.9414 (mtm) cc_final: 0.9028 (mtm)
REVERT: E  101 ARG cc_start: 0.8613 (ttt90) cc_final: 0.7222 (ptt180)
REVERT: F   81 GLU cc_start: 0.8803 (pp20) cc_final: 0.8247 (pp20)
REVERT: G   69 PHE cc_start: 0.8756 (m-10) cc_final: 0.8434 (m-10)
REVERT: G   74 ASP cc_start: 0.8774 (t0) cc_final: 0.8488 (t0)
REVERT: G   84 MET cc_start: 0.9310 (mtm) cc_final: 0.9044 (ttm)
REVERT: G  101 ARG cc_start: 0.8430 (ttt90) cc_final: 0.7149 (ptt180)
REVERT: J   66 ARG cc_start: 0.9420 (tpp80) cc_final: 0.9083 (tpp80)
REVERT: J   74 ASP cc_start: 0.8381 (t0) cc_final: 0.8090 (t0)
REVERT: J  101 ARG cc_start: 0.8592 (ttt90) cc_final: 0.7365 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1821
  time to fit residues: 74.4853
Evaluate side-chains
  232 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 143 optimal weight:    3.9990
   chunk 129 optimal weight:    3.9990
   chunk 133 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 117 optimal weight:    4.9990
   chunk 153 optimal weight:    8.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  38 HIS
B   3 HIS
B 104 HIS
D  61 ASN
E 104 HIS
F  38 HIS
F  61 ASN
G  46 GLN
G 104 HIS
** I  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  61 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.066736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2336 r_free = 0.2336 target = 0.050292 restraints weight = 83553.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2401 r_free = 0.2401 target = 0.053237 restraints weight = 34875.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2447 r_free = 0.2447 target = 0.055278 restraints weight = 19435.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.056701 restraints weight = 12593.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2502 r_free = 0.2502 target = 0.057717 restraints weight = 8961.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.2481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  13060  Z= 0.177
  Angle     :  0.529   4.307  17750  Z= 0.286
  Chirality :  0.044   0.128   1930
  Planarity :  0.004   0.056   2280
  Dihedral  :  3.895  15.187   1780
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  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: -2.01 (0.20), residues: 1615
  helix:  2.15 (0.68), residues: 55
  sheet: -0.69 (0.20), residues: 600
  loop : -2.06 (0.18), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  58 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.024   0.001   PHE B  69 
 TRP   0.013   0.001   TRP G 113 
 HIS   0.005   0.001   HIS F  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (13050)
  covalent geometry    : angle       0.52803 (17730)
  SS BOND              : bond        0.00349 (   10)
  SS BOND              : angle       1.06317 (   20)
  hydrogen bonds       : bond        0.04300 (  448)
  hydrogen bonds       : angle       5.81989 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   66 ARG cc_start: 0.9464 (tpp80) cc_final: 0.9031 (tpp80)
REVERT: H   74 ASP cc_start: 0.8542 (t0) cc_final: 0.8102 (t0)
REVERT: H   84 MET cc_start: 0.8657 (mmm) cc_final: 0.8089 (mmm)
REVERT: B   74 ASP cc_start: 0.8663 (t0) cc_final: 0.7971 (t0)
REVERT: B   77 LYS cc_start: 0.9309 (mtmm) cc_final: 0.9098 (mtmm)
REVERT: B   84 MET cc_start: 0.9501 (mtm) cc_final: 0.9181 (mtm)
REVERT: B   91 ASP cc_start: 0.8605 (m-30) cc_final: 0.8357 (m-30)
REVERT: E   48 THR cc_start: 0.9475 (m) cc_final: 0.9069 (t)
REVERT: E   53 ILE cc_start: 0.9269 (tt) cc_final: 0.9032 (tt)
REVERT: E   69 PHE cc_start: 0.8937 (m-10) cc_final: 0.8424 (m-10)
REVERT: E   74 ASP cc_start: 0.8363 (t0) cc_final: 0.7958 (t0)
REVERT: E   84 MET cc_start: 0.9349 (mtm) cc_final: 0.8845 (mtm)
REVERT: E  101 ARG cc_start: 0.8776 (ttt90) cc_final: 0.7391 (ptt180)
REVERT: F    4 MET cc_start: 0.9466 (mmp) cc_final: 0.9256 (mmp)
REVERT: F   81 GLU cc_start: 0.8937 (pp20) cc_final: 0.8281 (pp20)
REVERT: G   74 ASP cc_start: 0.8636 (t0) cc_final: 0.7975 (t0)
REVERT: G   77 LYS cc_start: 0.9328 (mtmm) cc_final: 0.9110 (mtmm)
REVERT: G   84 MET cc_start: 0.9214 (mtm) cc_final: 0.8873 (mtm)
REVERT: G  101 ARG cc_start: 0.8633 (ttt90) cc_final: 0.7155 (ptt180)
REVERT: I   81 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: J   74 ASP cc_start: 0.8353 (t0) cc_final: 0.8022 (t0)
REVERT: J  101 ARG cc_start: 0.8748 (ttt90) cc_final: 0.7378 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1865
  time to fit residues: 76.0811
Evaluate side-chains
  235 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   chunk 127 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 158 optimal weight:    9.9990
   chunk 147 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 151 optimal weight:    9.9990
   chunk 133 optimal weight:    0.8980
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 HIS
G   3 HIS
G  46 GLN
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.065045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2309 r_free = 0.2309 target = 0.049544 restraints weight = 82508.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2370 r_free = 0.2370 target = 0.052194 restraints weight = 36446.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2414 r_free = 0.2414 target = 0.054055 restraints weight = 20827.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.055348 restraints weight = 13666.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2465 r_free = 0.2465 target = 0.056264 restraints weight = 9859.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  13060  Z= 0.222
  Angle     :  0.556   4.979  17750  Z= 0.301
  Chirality :  0.044   0.126   1930
  Planarity :  0.004   0.067   2280
  Dihedral  :  4.105  17.436   1780
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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: -2.14 (0.19), residues: 1615
  helix:  1.89 (0.67), residues: 55
  sheet: -0.85 (0.20), residues: 595
  loop : -2.08 (0.18), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I  58 
 TYR   0.013   0.001   TYR D  40 
 PHE   0.030   0.001   PHE B  69 
 TRP   0.012   0.001   TRP G 113 
 HIS   0.008   0.001   HIS G   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (13050)
  covalent geometry    : angle       0.55488 (17730)
  SS BOND              : bond        0.00411 (   10)
  SS BOND              : angle       1.15282 (   20)
  hydrogen bonds       : bond        0.04547 (  448)
  hydrogen bonds       : angle       5.93447 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   66 ARG cc_start: 0.9554 (tpp80) cc_final: 0.9097 (tpp80)
REVERT: H   74 ASP cc_start: 0.8696 (t0) cc_final: 0.8283 (t0)
REVERT: H   84 MET cc_start: 0.8697 (mmm) cc_final: 0.8357 (mmm)
REVERT: B   74 ASP cc_start: 0.8712 (t0) cc_final: 0.8286 (t0)
REVERT: B   84 MET cc_start: 0.9463 (mtm) cc_final: 0.9082 (mtp)
REVERT: B   91 ASP cc_start: 0.8800 (m-30) cc_final: 0.8519 (m-30)
REVERT: D   81 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: E   40 ARG cc_start: 0.9061 (ttm170) cc_final: 0.8780 (ttm170)
REVERT: E   48 THR cc_start: 0.9497 (m) cc_final: 0.9116 (t)
REVERT: E   53 ILE cc_start: 0.9355 (tt) cc_final: 0.9097 (tt)
REVERT: E   74 ASP cc_start: 0.8524 (t0) cc_final: 0.8116 (t0)
REVERT: E   84 MET cc_start: 0.9192 (mtm) cc_final: 0.8774 (mtm)
REVERT: E  101 ARG cc_start: 0.8991 (ttt90) cc_final: 0.7550 (ptt180)
REVERT: F   81 GLU cc_start: 0.8942 (pp20) cc_final: 0.8329 (pp20)
REVERT: G   48 THR cc_start: 0.9536 (m) cc_final: 0.9191 (t)
REVERT: G   74 ASP cc_start: 0.8719 (t0) cc_final: 0.8288 (t0)
REVERT: G   84 MET cc_start: 0.9119 (mtm) cc_final: 0.8771 (mtm)
REVERT: G  101 ARG cc_start: 0.8936 (ttt90) cc_final: 0.7327 (ptt180)
REVERT: J   48 THR cc_start: 0.9543 (m) cc_final: 0.9179 (t)
REVERT: J   74 ASP cc_start: 0.8407 (t0) cc_final: 0.7874 (t0)
REVERT: J  101 ARG cc_start: 0.9036 (ttt90) cc_final: 0.7552 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1923
  time to fit residues: 72.1465
Evaluate side-chains
  224 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 145 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 152 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
H 104 HIS
B 104 HIS
E 104 HIS
G  46 GLN
G 104 HIS
** I  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  46 GLN
** J  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.065761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2317 r_free = 0.2317 target = 0.049497 restraints weight = 83002.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2383 r_free = 0.2383 target = 0.052419 restraints weight = 34702.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2428 r_free = 0.2428 target = 0.054449 restraints weight = 19374.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.055838 restraints weight = 12556.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.056850 restraints weight = 8969.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13060  Z= 0.178
  Angle     :  0.531   4.825  17750  Z= 0.286
  Chirality :  0.044   0.129   1930
  Planarity :  0.004   0.072   2280
  Dihedral  :  4.038  17.510   1780
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.14 %
    Favored  : 98.79 %
  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: -2.15 (0.19), residues: 1615
  helix:  1.82 (0.67), residues: 55
  sheet: -0.95 (0.20), residues: 625
  loop : -2.03 (0.18), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  58 
 TYR   0.011   0.001   TYR H  81 
 PHE   0.024   0.001   PHE B  69 
 TRP   0.009   0.001   TRP J 113 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (13050)
  covalent geometry    : angle       0.53015 (17730)
  SS BOND              : bond        0.00344 (   10)
  SS BOND              : angle       0.87755 (   20)
  hydrogen bonds       : bond        0.04226 (  448)
  hydrogen bonds       : angle       5.81367 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 291
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   66 ARG cc_start: 0.9509 (tpp80) cc_final: 0.9039 (tpp80)
REVERT: H   74 ASP cc_start: 0.8576 (t0) cc_final: 0.8137 (t0)
REVERT: A   62 GLU cc_start: 0.9163 (tp30) cc_final: 0.8669 (tp30)
REVERT: B   74 ASP cc_start: 0.8430 (t0) cc_final: 0.8011 (t0)
REVERT: B   84 MET cc_start: 0.9570 (mtm) cc_final: 0.8992 (mtp)
REVERT: B   91 ASP cc_start: 0.8707 (m-30) cc_final: 0.8436 (m-30)
REVERT: E   40 ARG cc_start: 0.8978 (ttm170) cc_final: 0.8596 (ttm170)
REVERT: E   48 THR cc_start: 0.9487 (m) cc_final: 0.9109 (t)
REVERT: E   53 ILE cc_start: 0.9295 (tt) cc_final: 0.9060 (tt)
REVERT: E   74 ASP cc_start: 0.8392 (t0) cc_final: 0.7986 (t0)
REVERT: E   84 MET cc_start: 0.9195 (mtm) cc_final: 0.8616 (mtm)
REVERT: E  101 ARG cc_start: 0.8954 (ttt90) cc_final: 0.7485 (ptt180)
REVERT: F   81 GLU cc_start: 0.8971 (pp20) cc_final: 0.8291 (pp20)
REVERT: G   38 TRP cc_start: 0.9213 (m100) cc_final: 0.7987 (m100)
REVERT: G   48 THR cc_start: 0.9528 (m) cc_final: 0.9204 (t)
REVERT: G   74 ASP cc_start: 0.8542 (t0) cc_final: 0.7794 (t0)
REVERT: G   84 MET cc_start: 0.9151 (mtm) cc_final: 0.8934 (mtm)
REVERT: G  101 ARG cc_start: 0.8900 (ttt90) cc_final: 0.7269 (ptt180)
REVERT: J   38 TRP cc_start: 0.9304 (m100) cc_final: 0.8019 (m100)
REVERT: J   48 THR cc_start: 0.9535 (m) cc_final: 0.9176 (t)
REVERT: J   74 ASP cc_start: 0.8346 (t0) cc_final: 0.8073 (t0)
REVERT: J  101 ARG cc_start: 0.8970 (ttt90) cc_final: 0.7509 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 292
  average time/residue: 0.1783
  time to fit residues: 74.6368
Evaluate side-chains
  230 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 89 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 112 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 116 optimal weight:    8.9990
   chunk 144 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
H 104 HIS
G  46 GLN
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  46 GLN
** J  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.065858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2314 r_free = 0.2314 target = 0.049997 restraints weight = 83407.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2376 r_free = 0.2376 target = 0.052693 restraints weight = 37198.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2417 r_free = 0.2417 target = 0.054524 restraints weight = 21391.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2448 r_free = 0.2448 target = 0.055853 restraints weight = 14219.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2469 r_free = 0.2469 target = 0.056785 restraints weight = 10360.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  13060  Z= 0.139
  Angle     :  0.513   4.594  17750  Z= 0.275
  Chirality :  0.044   0.132   1930
  Planarity :  0.004   0.073   2280
  Dihedral  :  3.933  16.809   1780
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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: -2.06 (0.19), residues: 1615
  helix:  1.82 (0.67), residues: 55
  sheet: -0.81 (0.20), residues: 595
  loop : -2.01 (0.18), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  58 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.018   0.001   PHE B  69 
 TRP   0.008   0.001   TRP G 113 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (13050)
  covalent geometry    : angle       0.51307 (17730)
  SS BOND              : bond        0.00327 (   10)
  SS BOND              : angle       0.73398 (   20)
  hydrogen bonds       : bond        0.03978 (  448)
  hydrogen bonds       : angle       5.69268 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 TRP cc_start: 0.9162 (m100) cc_final: 0.7768 (m100)
REVERT: H   66 ARG cc_start: 0.9507 (tpp80) cc_final: 0.9055 (tpp80)
REVERT: H   74 ASP cc_start: 0.8583 (t0) cc_final: 0.8152 (t0)
REVERT: B   38 TRP cc_start: 0.9259 (m100) cc_final: 0.7942 (m100)
REVERT: B   74 ASP cc_start: 0.8437 (t0) cc_final: 0.8000 (t0)
REVERT: B   84 MET cc_start: 0.9397 (mtm) cc_final: 0.8890 (mtp)
REVERT: B   91 ASP cc_start: 0.8700 (m-30) cc_final: 0.8426 (m-30)
REVERT: E   38 TRP cc_start: 0.9194 (m100) cc_final: 0.7933 (m100)
REVERT: E   48 THR cc_start: 0.9444 (m) cc_final: 0.9112 (t)
REVERT: E   53 ILE cc_start: 0.9314 (tt) cc_final: 0.9085 (tp)
REVERT: E   74 ASP cc_start: 0.8397 (t0) cc_final: 0.8007 (t0)
REVERT: E   84 MET cc_start: 0.9199 (mtm) cc_final: 0.8628 (mtm)
REVERT: E  101 ARG cc_start: 0.8957 (ttt90) cc_final: 0.7482 (ptt180)
REVERT: F   81 GLU cc_start: 0.8957 (pp20) cc_final: 0.8247 (pp20)
REVERT: G   38 TRP cc_start: 0.9199 (m100) cc_final: 0.7976 (m100)
REVERT: G   48 THR cc_start: 0.9526 (m) cc_final: 0.9198 (t)
REVERT: G   74 ASP cc_start: 0.8622 (t0) cc_final: 0.8227 (t0)
REVERT: G  101 ARG cc_start: 0.8862 (ttt90) cc_final: 0.7297 (ptt180)
REVERT: J   38 TRP cc_start: 0.9273 (m100) cc_final: 0.8041 (m100)
REVERT: J   48 THR cc_start: 0.9532 (m) cc_final: 0.9184 (t)
REVERT: J   53 ILE cc_start: 0.9256 (tt) cc_final: 0.9043 (tt)
REVERT: J   69 PHE cc_start: 0.8310 (m-80) cc_final: 0.8002 (m-80)
REVERT: J   74 ASP cc_start: 0.8497 (t0) cc_final: 0.8266 (t0)
REVERT: J  101 ARG cc_start: 0.8983 (ttt90) cc_final: 0.7522 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1926
  time to fit residues: 78.1974
Evaluate side-chains
  233 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 104 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 144 optimal weight:    3.9990
   chunk 109 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
C  38 HIS
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  46 GLN
G  46 GLN
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.064903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2309 r_free = 0.2309 target = 0.049508 restraints weight = 81879.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2369 r_free = 0.2369 target = 0.052180 restraints weight = 35645.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2411 r_free = 0.2411 target = 0.054063 restraints weight = 20116.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2438 r_free = 0.2438 target = 0.055279 restraints weight = 13054.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2460 r_free = 0.2460 target = 0.056226 restraints weight = 9479.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.2450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8696
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024  13060  Z= 0.206
  Angle     :  0.547   4.395  17750  Z= 0.295
  Chirality :  0.044   0.126   1930
  Planarity :  0.004   0.075   2280
  Dihedral  :  4.114  16.655   1780
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 20.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.79 %
    Favored  : 99.14 %
  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: -2.15 (0.19), residues: 1615
  helix:  1.73 (0.67), residues: 55
  sheet: -0.95 (0.20), residues: 620
  loop : -2.02 (0.18), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  58 
 TYR   0.011   0.001   TYR H  96 
 PHE   0.021   0.001   PHE B  69 
 TRP   0.011   0.001   TRP G 113 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (13050)
  covalent geometry    : angle       0.54590 (17730)
  SS BOND              : bond        0.00376 (   10)
  SS BOND              : angle       1.01278 (   20)
  hydrogen bonds       : bond        0.04358 (  448)
  hydrogen bonds       : angle       5.81111 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 TRP cc_start: 0.9248 (m100) cc_final: 0.7997 (m100)
REVERT: H   45 ASN cc_start: 0.8571 (t0) cc_final: 0.8134 (p0)
REVERT: H   74 ASP cc_start: 0.8620 (t0) cc_final: 0.8208 (t0)
REVERT: B   38 TRP cc_start: 0.9313 (m100) cc_final: 0.7989 (m100)
REVERT: B   74 ASP cc_start: 0.8563 (t0) cc_final: 0.8158 (t0)
REVERT: B   84 MET cc_start: 0.9423 (mtm) cc_final: 0.9211 (mtm)
REVERT: B   91 ASP cc_start: 0.8773 (m-30) cc_final: 0.8509 (m-30)
REVERT: E   38 TRP cc_start: 0.9264 (m100) cc_final: 0.7997 (m100)
REVERT: E   48 THR cc_start: 0.9492 (m) cc_final: 0.9133 (t)
REVERT: E   53 ILE cc_start: 0.9345 (tt) cc_final: 0.9119 (tt)
REVERT: E   74 ASP cc_start: 0.8545 (t0) cc_final: 0.8173 (t0)
REVERT: E   84 MET cc_start: 0.9169 (mtm) cc_final: 0.8484 (mtm)
REVERT: E  101 ARG cc_start: 0.9051 (ttt90) cc_final: 0.7561 (ptt180)
REVERT: G   38 TRP cc_start: 0.9265 (m100) cc_final: 0.8089 (m100)
REVERT: G   48 THR cc_start: 0.9525 (m) cc_final: 0.9211 (t)
REVERT: G   74 ASP cc_start: 0.8602 (t0) cc_final: 0.8199 (t0)
REVERT: G  101 ARG cc_start: 0.9021 (ttt90) cc_final: 0.7338 (ptt180)
REVERT: J   38 TRP cc_start: 0.9319 (m100) cc_final: 0.8108 (m100)
REVERT: J   48 THR cc_start: 0.9535 (m) cc_final: 0.9190 (t)
REVERT: J   74 ASP cc_start: 0.8493 (t0) cc_final: 0.8227 (t0)
REVERT: J  101 ARG cc_start: 0.9090 (ttt90) cc_final: 0.7571 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1897
  time to fit residues: 68.6127
Evaluate side-chains
  225 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 144 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 121 optimal weight:    8.9990
   chunk 138 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 148 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
C  38 HIS
** H  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 ASN
H 104 HIS
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 HIS
E  46 GLN
** E  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  46 GLN
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  46 GLN
** J  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.065493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2314 r_free = 0.2314 target = 0.049320 restraints weight = 82813.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2380 r_free = 0.2380 target = 0.052242 restraints weight = 34032.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2425 r_free = 0.2425 target = 0.054261 restraints weight = 18868.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.055706 restraints weight = 12208.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.056645 restraints weight = 8674.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13060  Z= 0.154
  Angle     :  0.520   4.222  17750  Z= 0.279
  Chirality :  0.043   0.129   1930
  Planarity :  0.004   0.078   2280
  Dihedral  :  3.983  15.651   1780
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 19.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.50 %
    Favored  : 99.36 %
  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: -2.09 (0.20), residues: 1615
  helix:  1.79 (0.67), residues: 55
  sheet: -0.76 (0.20), residues: 595
  loop : -2.07 (0.18), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I  58 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.018   0.001   PHE B  69 
 TRP   0.009   0.001   TRP E 113 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13050)
  covalent geometry    : angle       0.52011 (17730)
  SS BOND              : bond        0.00339 (   10)
  SS BOND              : angle       0.76260 (   20)
  hydrogen bonds       : bond        0.04032 (  448)
  hydrogen bonds       : angle       5.68666 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 257
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 TRP cc_start: 0.9219 (m100) cc_final: 0.7768 (m100)
REVERT: H   45 ASN cc_start: 0.8716 (t0) cc_final: 0.8142 (p0)
REVERT: H   74 ASP cc_start: 0.8511 (t0) cc_final: 0.8082 (t0)
REVERT: H   84 MET cc_start: 0.9052 (mmm) cc_final: 0.8827 (mmm)
REVERT: B   38 TRP cc_start: 0.9339 (m100) cc_final: 0.7892 (m100)
REVERT: B   74 ASP cc_start: 0.8428 (t0) cc_final: 0.8008 (t0)
REVERT: B   84 MET cc_start: 0.9499 (mtm) cc_final: 0.9020 (mtm)
REVERT: B   91 ASP cc_start: 0.8684 (m-30) cc_final: 0.8406 (m-30)
REVERT: E   38 TRP cc_start: 0.9276 (m100) cc_final: 0.7839 (m100)
REVERT: E   48 THR cc_start: 0.9485 (m) cc_final: 0.9149 (t)
REVERT: E   53 ILE cc_start: 0.9253 (tt) cc_final: 0.9030 (tt)
REVERT: E   74 ASP cc_start: 0.8357 (t0) cc_final: 0.7969 (t0)
REVERT: E   84 MET cc_start: 0.9211 (mtm) cc_final: 0.8535 (mtm)
REVERT: E   91 ASP cc_start: 0.9116 (m-30) cc_final: 0.8756 (m-30)
REVERT: E  101 ARG cc_start: 0.8976 (ttt90) cc_final: 0.7492 (ptt180)
REVERT: G   38 TRP cc_start: 0.9242 (m100) cc_final: 0.7941 (m100)
REVERT: G   46 GLN cc_start: 0.8257 (pt0) cc_final: 0.8044 (tt0)
REVERT: G   48 THR cc_start: 0.9535 (m) cc_final: 0.9251 (t)
REVERT: G   74 ASP cc_start: 0.8495 (t0) cc_final: 0.7964 (t0)
REVERT: G  101 ARG cc_start: 0.8916 (ttt90) cc_final: 0.7279 (ptt180)
REVERT: J   38 TRP cc_start: 0.9326 (m100) cc_final: 0.8038 (m100)
REVERT: J   48 THR cc_start: 0.9528 (m) cc_final: 0.9165 (t)
REVERT: J   74 ASP cc_start: 0.8294 (t0) cc_final: 0.8032 (t0)
REVERT: J  101 ARG cc_start: 0.8995 (ttt90) cc_final: 0.7516 (ptt180)
  outliers start: 2
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1938
  time to fit residues: 72.5737
Evaluate side-chains
  229 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 116 optimal weight:    7.9990
   chunk 147 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 143 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  38 HIS
** H  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  46 GLN
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.064556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2297 r_free = 0.2297 target = 0.049107 restraints weight = 83196.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2358 r_free = 0.2358 target = 0.051762 restraints weight = 36601.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2400 r_free = 0.2400 target = 0.053609 restraints weight = 20877.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2429 r_free = 0.2429 target = 0.054896 restraints weight = 13727.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2448 r_free = 0.2448 target = 0.055746 restraints weight = 9916.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.2440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027  13060  Z= 0.221
  Angle     :  0.557   5.260  17750  Z= 0.300
  Chirality :  0.044   0.123   1930
  Planarity :  0.004   0.070   2280
  Dihedral  :  4.156  16.738   1780
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 21.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.36 %
    Favored  : 99.57 %
  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: -2.18 (0.19), residues: 1615
  helix:  1.71 (0.67), residues: 55
  sheet: -0.94 (0.20), residues: 620
  loop : -2.07 (0.18), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG I  58 
 TYR   0.011   0.001   TYR H  96 
 PHE   0.019   0.001   PHE B  69 
 TRP   0.010   0.001   TRP G 113 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (13050)
  covalent geometry    : angle       0.55652 (17730)
  SS BOND              : bond        0.00377 (   10)
  SS BOND              : angle       0.99256 (   20)
  hydrogen bonds       : bond        0.04389 (  448)
  hydrogen bonds       : angle       5.79744 ( 1071)

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

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

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3230 Ramachandran restraints generated.
    1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 TRP cc_start: 0.9254 (m100) cc_final: 0.7964 (m100)
REVERT: H   45 ASN cc_start: 0.8762 (t0) cc_final: 0.8138 (p0)
REVERT: H   74 ASP cc_start: 0.8676 (t0) cc_final: 0.8263 (t0)
REVERT: H   84 MET cc_start: 0.9012 (mmm) cc_final: 0.8811 (mmm)
REVERT: A   16 ASP cc_start: 0.9249 (p0) cc_final: 0.9035 (p0)
REVERT: B   38 TRP cc_start: 0.9318 (m100) cc_final: 0.8026 (m100)
REVERT: B   74 ASP cc_start: 0.8662 (t0) cc_final: 0.8280 (t0)
REVERT: B   84 MET cc_start: 0.9397 (mtm) cc_final: 0.9005 (mtm)
REVERT: B   91 ASP cc_start: 0.8781 (m-30) cc_final: 0.8515 (m-30)
REVERT: E   38 TRP cc_start: 0.9280 (m100) cc_final: 0.7979 (m100)
REVERT: E   48 THR cc_start: 0.9477 (m) cc_final: 0.9106 (t)
REVERT: E   53 ILE cc_start: 0.9340 (tt) cc_final: 0.9114 (tt)
REVERT: E   74 ASP cc_start: 0.8515 (t0) cc_final: 0.8148 (t0)
REVERT: E   84 MET cc_start: 0.9148 (mtm) cc_final: 0.8502 (mtm)
REVERT: E   91 ASP cc_start: 0.9097 (m-30) cc_final: 0.8835 (m-30)
REVERT: E  101 ARG cc_start: 0.9074 (ttt90) cc_final: 0.7613 (ptt180)
REVERT: G   38 TRP cc_start: 0.9261 (m100) cc_final: 0.8049 (m100)
REVERT: G   48 THR cc_start: 0.9538 (m) cc_final: 0.9242 (t)
REVERT: G   74 ASP cc_start: 0.8635 (t0) cc_final: 0.7643 (t0)
REVERT: G   84 MET cc_start: 0.9033 (mtm) cc_final: 0.8663 (mtm)
REVERT: G  101 ARG cc_start: 0.9018 (ttt90) cc_final: 0.7375 (ptt180)
REVERT: J   38 TRP cc_start: 0.9334 (m100) cc_final: 0.8194 (m100)
REVERT: J   45 ASN cc_start: 0.8695 (t0) cc_final: 0.7892 (p0)
REVERT: J   48 THR cc_start: 0.9529 (m) cc_final: 0.9146 (t)
REVERT: J   74 ASP cc_start: 0.8477 (t0) cc_final: 0.8248 (t0)
REVERT: J  101 ARG cc_start: 0.9103 (ttt90) cc_final: 0.7589 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1926
  time to fit residues: 68.0997
Evaluate side-chains
  226 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 154 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C  38 HIS
** H  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 104 HIS
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 HIS
G   3 HIS
** G  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 HIS
** J  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.066586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2342 r_free = 0.2342 target = 0.051099 restraints weight = 81600.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2402 r_free = 0.2402 target = 0.053831 restraints weight = 35328.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.055692 restraints weight = 19953.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2473 r_free = 0.2473 target = 0.057019 restraints weight = 13020.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.057970 restraints weight = 9335.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.2488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13060  Z= 0.095
  Angle     :  0.503   4.418  17750  Z= 0.266
  Chirality :  0.044   0.136   1930
  Planarity :  0.004   0.096   2280
  Dihedral  :  3.845  14.992   1780
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.21 %
    Favored  : 99.71 %
  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: -2.02 (0.20), residues: 1615
  helix:  1.80 (0.67), residues: 55
  sheet: -0.85 (0.20), residues: 630
  loop : -1.95 (0.19), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG I  58 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.014   0.001   PHE B  69 
 TRP   0.008   0.001   TRP I 110 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (13050)
  covalent geometry    : angle       0.50277 (17730)
  SS BOND              : bond        0.00267 (   10)
  SS BOND              : angle       0.47073 (   20)
  hydrogen bonds       : bond        0.03564 (  448)
  hydrogen bonds       : angle       5.44684 ( 1071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2871.15 seconds
wall clock time: 50 minutes 6.07 seconds (3006.07 seconds total)