Starting phenix.real_space_refine
on Tue Feb 11 10:15:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cq7_45810/02_2025/9cq7_45810.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cq7_45810/02_2025/9cq7_45810.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cq7_45810/02_2025/9cq7_45810.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cq7_45810/02_2025/9cq7_45810.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cq7_45810/02_2025/9cq7_45810.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cq7_45810/02_2025/9cq7_45810.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    3319      2.51       5
     N     859      2.21       5
     O    1021      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5222
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "D"
      Number of atoms: 1611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1611
          Classifications: {'peptide': 206}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "G"
      Number of atoms: 1837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1837
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 12, 'TRANS': 218}
    Chain: "H"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 930
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 5, 'TRANS': 113}
    Chain: "I"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 788
          Classifications: {'peptide': 104}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 99}
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.64, per 1000 atoms: 0.89
  Number of scatterers: 5222
  At special positions: 0
  Unit cell: (72.154, 88.934, 101.519, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1021      8.00
     N     859      7.00
     C    3319      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 140 " - pdb=" SG  CYS D 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 154 " - pdb=" SG  CYS G 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  23 " - pdb=" SG  CYS I  87 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG D 301 " - " ASN D 197 "
      " NAG G 301 " - " ASN G 188 "
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 550.3 milliseconds
  

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1222

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 20 sheets defined
      3.3% alpha, 42.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'G' and resid 143 through 148
    Processing helix  chain 'G' and resid 200 through 205
      removed outlier: 4.024A  pdb=" N   ASP G 205 " --> pdb=" O   GLU G 201 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 217 through 221
      removed outlier: 3.505A  pdb=" N   GLY G 220 " --> pdb=" O   ASN G 217 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 78 through 82
      removed outlier: 3.640A  pdb=" N   ALA I  82 " --> pdb=" O   ALA I  79 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6
      removed outlier: 3.899A  pdb=" N   GLU D   3 " --> pdb=" O   LYS D  26 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ASP D  69 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 13 through 14
      removed outlier: 6.813A  pdb=" N   VAL D  13 " --> pdb=" O   GLU D 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 48
      removed outlier: 3.539A  pdb=" N   ALA D  93 " --> pdb=" O   ASN D  36 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER D  89 " --> pdb=" O   LYS D  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 47 through 48
      removed outlier: 3.539A  pdb=" N   ALA D  93 " --> pdb=" O   ASN D  36 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER D  89 " --> pdb=" O   LYS D  40 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 51
      removed outlier: 4.280A  pdb=" N   ILE D  55 " --> pdb=" O   ARG D  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 133 through 134
      removed outlier: 3.850A  pdb=" N   ASN D 137 " --> pdb=" O   ASN D 134 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS D 179 " --> pdb=" O   CYS D 140 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL D 142 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLU D 144 " --> pdb=" O   TYR D 175 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   TYR D 175 " --> pdb=" O   GLU D 144 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL D 178 " --> pdb=" O   ALA D 166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 151 through 154
      removed outlier: 3.871A  pdb=" N   ASN D 153 " --> pdb=" O   SER D 192 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   SER D 192 " --> pdb=" O   ASN D 153 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 5
    Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 14
      removed outlier: 5.629A  pdb=" N   SER G  11 " --> pdb=" O   ILE G 120 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   THR G 122 " --> pdb=" O   SER G  11 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LYS G  13 " --> pdb=" O   THR G 122 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 58 through 59
      removed outlier: 6.714A  pdb=" N   TRP G  37 " --> pdb=" O   LEU G  49 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   SER G  51 " --> pdb=" O   VAL G  35 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL G  35 " --> pdb=" O   SER G  51 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 135 through 137
      removed outlier: 3.515A  pdb=" N   PHE G 137 " --> pdb=" O   LEU G 153 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU G 153 " --> pdb=" O   PHE G 137 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER G 195 " --> pdb=" O   CYS G 154 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   TYR G 191 " --> pdb=" O   LYS G 158 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 135 through 137
      removed outlier: 3.515A  pdb=" N   PHE G 137 " --> pdb=" O   LEU G 153 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU G 153 " --> pdb=" O   PHE G 137 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER G 195 " --> pdb=" O   CYS G 154 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   TYR G 191 " --> pdb=" O   LYS G 158 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   MET G 192 " --> pdb=" O   MET G 185 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   MET G 185 " --> pdb=" O   MET G 192 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 150 through 151
    Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 170
      removed outlier: 4.306A  pdb=" N   GLN G 169 " --> pdb=" O   ARG G 209 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ARG G 209 " --> pdb=" O   GLN G 169 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE G 225 " --> pdb=" O   CYS G 210 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL G 212 " --> pdb=" O   GLN G 223 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.516A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 9 through 11
      removed outlier: 3.510A  pdb=" N   THR H 118 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   ASN H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 9 through 11
      removed outlier: 3.510A  pdb=" N   THR H 118 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   TYR H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'I' and resid 4 through 5
      removed outlier: 3.545A  pdb=" N   ILE I  19 " --> pdb=" O   ILE I  74 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE I  69 " --> pdb=" O   SER I  66 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12
      removed outlier: 3.606A  pdb=" N   MET I  11 " --> pdb=" O   LYS I 101 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLU I 103 " --> pdb=" O   MET I  11 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   MET I  32 " --> pdb=" O   TYR I  48 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   TYR I  48 " --> pdb=" O   MET I  32 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   TRP I  34 " --> pdb=" O   LEU I  46 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 12
      removed outlier: 3.606A  pdb=" N   MET I  11 " --> pdb=" O   LYS I 101 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLU I 103 " --> pdb=" O   MET I  11 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN I  89 " --> pdb=" O   THR I  95 " (cutoff:3.500A)

    174 hydrogen bonds defined for protein.
    408 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.50

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1640
        1.34 -     1.46: 1279
        1.46 -     1.58: 2391
        1.58 -     1.70: 0
        1.70 -     1.82: 33
  Bond restraints: 5343
  Sorted by residual:
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.40e+00
  bond pdb=" C1  NAG G 301 "
       pdb=" O5  NAG G 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" C1  NAG D 301 "
       pdb=" O5  NAG D 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.63e+00
  bond pdb=" C5  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.25e+00
  bond pdb=" C5  NAG G 301 "
       pdb=" O5  NAG G 301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.22e+00
  ... (remaining 5338 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 6948
        1.37 -     2.74: 236
        2.74 -     4.11: 47
        4.11 -     5.48: 13
        5.48 -     6.85: 2
  Bond angle restraints: 7246
  Sorted by residual:
  angle pdb=" C   ALA G 128 "
        pdb=" N   ASP G 129 "
        pdb=" CA  ASP G 129 "
      ideal   model   delta    sigma   weight residual
     122.82  127.10   -4.28 1.42e+00 4.96e-01 9.07e+00
  angle pdb=" N   GLY H  44 "
        pdb=" CA  GLY H  44 "
        pdb=" C   GLY H  44 "
      ideal   model   delta    sigma   weight residual
     113.18  107.66    5.52 2.37e+00 1.78e-01 5.42e+00
  angle pdb=" C   LYS D 143 "
        pdb=" N   GLU D 144 "
        pdb=" CA  GLU D 144 "
      ideal   model   delta    sigma   weight residual
     123.34  119.18    4.16 1.80e+00 3.09e-01 5.34e+00
  angle pdb=" CA  THR I  50 "
        pdb=" CB  THR I  50 "
        pdb=" CG2 THR I  50 "
      ideal   model   delta    sigma   weight residual
     110.50  114.10   -3.60 1.70e+00 3.46e-01 4.49e+00
  angle pdb=" C   LYS G  68 "
        pdb=" N   PHE G  69 "
        pdb=" CA  PHE G  69 "
      ideal   model   delta    sigma   weight residual
     121.54  125.53   -3.99 1.91e+00 2.74e-01 4.36e+00
  ... (remaining 7241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 2922
       16.90 -    33.79: 263
       33.79 -    50.69: 46
       50.69 -    67.59: 13
       67.59 -    84.49: 12
  Dihedral angle restraints: 3256
    sinusoidal: 1343
      harmonic: 1913
  Sorted by residual:
  dihedral pdb=" CB  CYS D 140 "
           pdb=" SG  CYS D 140 "
           pdb=" SG  CYS D 191 "
           pdb=" CB  CYS D 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.45   72.55     1      1.00e+01 1.00e-02 6.72e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  92 "
           pdb=" CB  CYS D  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.59   61.41     1      1.00e+01 1.00e-02 5.01e+01
  dihedral pdb=" CA  VAL D 142 "
           pdb=" C   VAL D 142 "
           pdb=" N   LYS D 143 "
           pdb=" CA  LYS D 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.16  -22.84     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 3253 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 698
       0.063 -    0.126: 107
       0.126 -    0.189: 10
       0.189 -    0.252: 0
       0.252 -    0.315: 1
  Chirality restraints: 816
  Sorted by residual:
  chirality pdb=" CB  ILE D  55 "
            pdb=" CA  ILE D  55 "
            pdb=" CG1 ILE D  55 "
            pdb=" CG2 ILE D  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" C1  NAG D 301 "
            pdb=" ND2 ASN D 197 "
            pdb=" C2  NAG D 301 "
            pdb=" O5  NAG D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" CA  THR I  50 "
            pdb=" N   THR I  50 "
            pdb=" C   THR I  50 "
            pdb=" CB  THR I  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.87e-01
  ... (remaining 813 not shown)

  Planarity restraints: 912
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG H  40 "   -0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO H  41 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL I  57 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO I  58 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO I  58 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO I  58 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I  96 "    0.009 2.00e-02 2.50e+03   1.22e-02 2.62e+00
        pdb=" CG  PHE I  96 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE I  96 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE I  96 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE I  96 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE I  96 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE I  96 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 909 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 118
        2.69 -     3.24: 4907
        3.24 -     3.79: 7535
        3.79 -     4.35: 10310
        4.35 -     4.90: 17533
  Nonbonded interactions: 40403
  Sorted by model distance:
  nonbonded pdb=" O   THR I  50 "
            pdb=" OG  SER I  51 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OE1 GLN G   6 "
            pdb=" OG1 THR G 117 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   LYS D 143 "
            pdb=" ND2 ASN D 176 "
     model   vdw
     2.170 3.120
  nonbonded pdb=" OG1 THR G 187 "
            pdb=" O   THR G 190 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OD1 ASP H  89 "
     model   vdw
     2.277 3.040
  ... (remaining 40398 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.190
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.610
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
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      :  0.003   0.031   5343  Z= 0.225
  Angle     :  0.622   6.848   7246  Z= 0.322
  Chirality :  0.047   0.315    816
  Planarity :  0.004   0.053    910
  Dihedral  : 14.051  84.486   2016
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.33), residues: 652
  helix:  None (None), residues: 0
  sheet:  0.43 (0.35), residues: 251
  loop : -1.10 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G 196 
 HIS   0.003   0.001   HIS I  33 
 PHE   0.028   0.002   PHE I  96 
 TYR   0.011   0.001   TYR D  90 
 ARG   0.002   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G    5 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7427 (tp30)
REVERT: G  133 LYS cc_start: 0.7467 (mmmt) cc_final: 0.7187 (mmtm)
REVERT: G  185 MET cc_start: 0.6600 (mpp) cc_final: 0.5901 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1944
  time to fit residues: 24.2169
Evaluate side-chains
  71 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0370
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0020
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4266

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

Flipped N/Q/H residues before XYZ refinement:
D  73 ASN
G 169 GLN
H  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.194647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.158496 restraints weight = 6426.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.99
r_work: 0.3740 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5343  Z= 0.213
  Angle     :  0.644   6.171   7246  Z= 0.344
  Chirality :  0.048   0.197    816
  Planarity :  0.005   0.047    910
  Dihedral  :  5.634  33.360    793
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  7.28 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet:  0.43 (0.34), residues: 260
  loop : -1.06 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 196 
 HIS   0.005   0.001   HIS G 167 
 PHE   0.018   0.002   PHE I  96 
 TYR   0.018   0.001   TYR D  90 
 ARG   0.010   0.001   ARG G 213 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 TYR cc_start: 0.7810 (m-80) cc_final: 0.6953 (m-80)
REVERT: D   80 LEU cc_start: 0.7381 (mm) cc_final: 0.7014 (mm)
REVERT: D  105 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (p0)
REVERT: G    5 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7856 (tp30)
REVERT: G  133 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7528 (mmtt)
REVERT: H   23 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7633 (tptm)
  outliers start: 17
  outliers final: 12
  residues processed: 86
  average time/residue: 0.1526
  time to fit residues: 17.6338
Evaluate side-chains
  85 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  105 ASP
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain G residue   86 ASN
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Chi-restraints excluded: chain I residue   41 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
G  47 GLN
G 167 HIS
H  39 GLN
H  82 GLN
I  37 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.191358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.156312 restraints weight = 6517.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 2.88
r_work: 0.3721 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5343  Z= 0.255
  Angle     :  0.626   5.507   7246  Z= 0.334
  Chirality :  0.048   0.202    816
  Planarity :  0.004   0.048    910
  Dihedral  :  5.535  30.382    793
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 11.27 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.33), residues: 652
  helix:  None (None), residues: 0
  sheet:  0.21 (0.33), residues: 267
  loop : -0.99 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP G 168 
 HIS   0.005   0.001   HIS G 167 
 PHE   0.021   0.002   PHE I  96 
 TYR   0.017   0.002   TYR D  90 
 ARG   0.011   0.001   ARG G 213 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 TYR cc_start: 0.7799 (m-80) cc_final: 0.6873 (m-80)
REVERT: G    5 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7738 (tp30)
REVERT: G  133 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7520 (mmtm)
REVERT: G  213 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7431 (mpp-170)
REVERT: H   81 MET cc_start: 0.7843 (ttt) cc_final: 0.7283 (ttt)
  outliers start: 18
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1650
  time to fit residues: 16.5825
Evaluate side-chains
  84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Chi-restraints excluded: chain I residue   41 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.190608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.155800 restraints weight = 6576.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 2.88
r_work: 0.3718 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5343  Z= 0.220
  Angle     :  0.592   5.563   7246  Z= 0.316
  Chirality :  0.047   0.198    816
  Planarity :  0.004   0.048    910
  Dihedral  :  5.322  24.709    793
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 13.86 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.33), residues: 652
  helix:  None (None), residues: 0
  sheet:  0.16 (0.33), residues: 267
  loop : -0.94 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 168 
 HIS   0.004   0.001   HIS G 167 
 PHE   0.016   0.002   PHE I  96 
 TYR   0.017   0.001   TYR D  50 
 ARG   0.003   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.473 
Fit side-chains
REVERT: D   33 TYR cc_start: 0.7793 (m-80) cc_final: 0.6960 (m-80)
REVERT: D  132 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6262 (ptt)
REVERT: G  101 GLU cc_start: 0.7044 (pt0) cc_final: 0.6828 (pp20)
REVERT: G  133 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7685 (mmtt)
REVERT: G  213 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.7439 (tpp80)
REVERT: H   23 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7645 (tptm)
REVERT: H   81 MET cc_start: 0.7919 (ttt) cc_final: 0.7512 (ttt)
  outliers start: 19
  outliers final: 16
  residues processed: 84
  average time/residue: 0.1686
  time to fit residues: 18.9736
Evaluate side-chains
  89 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue   86 ASN
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Chi-restraints excluded: chain I residue   41 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
G 125 GLN
G 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.189821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.155248 restraints weight = 6551.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.85
r_work: 0.3712 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5343  Z= 0.224
  Angle     :  0.592   5.553   7246  Z= 0.316
  Chirality :  0.047   0.205    816
  Planarity :  0.004   0.049    910
  Dihedral  :  5.266  22.228    793
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.42 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet:  0.03 (0.33), residues: 262
  loop : -0.98 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 196 
 HIS   0.003   0.001   HIS G 167 
 PHE   0.015   0.002   PHE I  96 
 TYR   0.009   0.001   TYR H  95 
 ARG   0.003   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.638 
Fit side-chains
REVERT: D   33 TYR cc_start: 0.7814 (m-80) cc_final: 0.7019 (m-80)
REVERT: D  132 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6254 (ptt)
REVERT: G  213 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7493 (tpp80)
REVERT: G  225 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6726 (tp)
REVERT: H   23 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7673 (tptm)
REVERT: H   46 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7366 (mp0)
REVERT: H   81 MET cc_start: 0.8004 (ttt) cc_final: 0.7569 (ttt)
  outliers start: 24
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1567
  time to fit residues: 17.5493
Evaluate side-chains
  84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain G residue  225 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Chi-restraints excluded: chain I residue   41 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 60 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
G 167 HIS
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.187034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.153286 restraints weight = 6503.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.71
r_work: 0.3678 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5343  Z= 0.310
  Angle     :  0.643   5.757   7246  Z= 0.344
  Chirality :  0.049   0.193    816
  Planarity :  0.005   0.047    910
  Dihedral  :  5.457  22.583    793
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 16.29 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet:  0.02 (0.33), residues: 257
  loop : -1.10 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G 168 
 HIS   0.003   0.001   HIS G 208 
 PHE   0.022   0.002   PHE I  96 
 TYR   0.018   0.002   TYR D  50 
 ARG   0.004   0.001   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
REVERT: D    3 GLU cc_start: 0.8033 (tt0) cc_final: 0.7562 (tt0)
REVERT: D   33 TYR cc_start: 0.7889 (m-80) cc_final: 0.6870 (m-80)
REVERT: D  132 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6112 (ptt)
REVERT: G  213 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7525 (tpp80)
REVERT: G  225 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6733 (tp)
REVERT: H   23 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7682 (tptm)
REVERT: H   46 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7533 (mt-10)
REVERT: H   81 MET cc_start: 0.8138 (ttt) cc_final: 0.7690 (ttt)
  outliers start: 25
  outliers final: 20
  residues processed: 82
  average time/residue: 0.1572
  time to fit residues: 17.2165
Evaluate side-chains
  92 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain G residue   45 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue   86 ASN
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain G residue  225 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Chi-restraints excluded: chain I residue   41 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.188133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.154963 restraints weight = 6459.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 2.68
r_work: 0.3700 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5343  Z= 0.246
  Angle     :  0.606   5.684   7246  Z= 0.325
  Chirality :  0.048   0.227    816
  Planarity :  0.004   0.049    910
  Dihedral  :  5.322  22.541    793
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 17.85 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet: -0.00 (0.33), residues: 257
  loop : -1.09 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP G 196 
 HIS   0.003   0.001   HIS G 208 
 PHE   0.016   0.002   PHE G  69 
 TYR   0.009   0.001   TYR H  95 
 ARG   0.005   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: D    3 GLU cc_start: 0.7977 (tt0) cc_final: 0.7560 (tt0)
REVERT: D   33 TYR cc_start: 0.7897 (m-80) cc_final: 0.6954 (m-80)
REVERT: D  132 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6120 (ptt)
REVERT: G  213 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7522 (tpp80)
REVERT: G  225 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6737 (tp)
REVERT: H   23 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7801 (tppt)
REVERT: H   46 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7259 (mp0)
REVERT: H   81 MET cc_start: 0.8062 (ttt) cc_final: 0.7584 (ttt)
  outliers start: 27
  outliers final: 20
  residues processed: 83
  average time/residue: 0.1596
  time to fit residues: 17.7139
Evaluate side-chains
  89 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain G residue   45 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain G residue  225 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 48 optimal weight:    0.3980
   chunk 0 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.188512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155355 restraints weight = 6440.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.68
r_work: 0.3708 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5343  Z= 0.226
  Angle     :  0.599   5.881   7246  Z= 0.321
  Chirality :  0.047   0.206    816
  Planarity :  0.004   0.049    910
  Dihedral  :  5.247  22.139    793
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 18.37 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet: -0.01 (0.33), residues: 257
  loop : -1.09 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 196 
 HIS   0.002   0.001   HIS G 208 
 PHE   0.015   0.002   PHE G  69 
 TYR   0.018   0.001   TYR D  50 
 ARG   0.004   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
REVERT: D    3 GLU cc_start: 0.8012 (tt0) cc_final: 0.7541 (tt0)
REVERT: D   33 TYR cc_start: 0.7901 (m-80) cc_final: 0.6960 (m-80)
REVERT: D  132 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6161 (ptt)
REVERT: G  213 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7481 (tpp80)
REVERT: G  225 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6725 (tp)
REVERT: H   23 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7776 (tppt)
REVERT: H   46 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7234 (mp0)
REVERT: H   81 MET cc_start: 0.8062 (ttt) cc_final: 0.7551 (ttt)
REVERT: I   11 MET cc_start: 0.6151 (ppp) cc_final: 0.5434 (ppp)
  outliers start: 24
  outliers final: 20
  residues processed: 82
  average time/residue: 0.1849
  time to fit residues: 19.7298
Evaluate side-chains
  88 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain G residue   45 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain G residue  225 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   chunk 36 optimal weight:    0.2980
   chunk 61 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
G 216 ASN
H  39 GLN
** I   6 GLN ** 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 = 0.4190 r_free = 0.4190 target = 0.188912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.155741 restraints weight = 6480.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.68
r_work: 0.3709 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5343  Z= 0.225
  Angle     :  0.594   5.742   7246  Z= 0.318
  Chirality :  0.047   0.196    816
  Planarity :  0.004   0.050    910
  Dihedral  :  5.170  22.293    793
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.89 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet: -0.04 (0.33), residues: 258
  loop : -1.06 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 196 
 HIS   0.002   0.001   HIS G 208 
 PHE   0.014   0.002   PHE G  69 
 TYR   0.010   0.001   TYR H  95 
 ARG   0.004   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
REVERT: D    3 GLU cc_start: 0.8025 (tt0) cc_final: 0.7547 (tt0)
REVERT: D   33 TYR cc_start: 0.7877 (m-80) cc_final: 0.7174 (m-80)
REVERT: D  132 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6101 (ptt)
REVERT: G  213 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7522 (tpp80)
REVERT: G  225 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6703 (tp)
REVERT: H   23 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7813 (tppt)
REVERT: H   46 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7273 (mp0)
REVERT: H   81 MET cc_start: 0.8049 (ttt) cc_final: 0.7530 (ttt)
REVERT: I   11 MET cc_start: 0.6061 (ppp) cc_final: 0.5485 (ppp)
  outliers start: 23
  outliers final: 19
  residues processed: 78
  average time/residue: 0.1815
  time to fit residues: 18.2445
Evaluate side-chains
  88 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain G residue   45 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain G residue  225 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** D  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.187182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153709 restraints weight = 6546.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.68
r_work: 0.3685 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5343  Z= 0.273
  Angle     :  0.629   5.722   7246  Z= 0.336
  Chirality :  0.048   0.213    816
  Planarity :  0.004   0.048    910
  Dihedral  :  5.323  22.850    793
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.89 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet: -0.09 (0.33), residues: 253
  loop : -1.10 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G 168 
 HIS   0.003   0.001   HIS G 208 
 PHE   0.015   0.002   PHE G  69 
 TYR   0.019   0.001   TYR D  50 
 ARG   0.005   0.000   ARG I  60 

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

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

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1304 Ramachandran restraints generated.
    652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: D    3 GLU cc_start: 0.8105 (tt0) cc_final: 0.7622 (tt0)
REVERT: D   26 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7374 (mttm)
REVERT: D  132 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6179 (ptt)
REVERT: G  213 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7527 (mpp-170)
REVERT: G  225 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6709 (tp)
REVERT: H   23 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7678 (tptm)
REVERT: H   46 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7375 (mp0)
REVERT: H   81 MET cc_start: 0.8126 (ttt) cc_final: 0.7638 (ttt)
REVERT: I   11 MET cc_start: 0.6106 (ppp) cc_final: 0.5636 (ppp)
  outliers start: 25
  outliers final: 20
  residues processed: 81
  average time/residue: 0.1932
  time to fit residues: 20.4650
Evaluate side-chains
  87 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  132 MET
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain G residue   45 VAL
Chi-restraints excluded: chain G residue   80 SER
Chi-restraints excluded: chain G residue  141 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  177 LEU
Chi-restraints excluded: chain G residue  212 VAL
Chi-restraints excluded: chain G residue  225 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   32 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.187770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.154584 restraints weight = 6519.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 2.67
r_work: 0.3705 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5343  Z= 0.246
  Angle     :  0.611   5.687   7246  Z= 0.327
  Chirality :  0.047   0.196    816
  Planarity :  0.004   0.050    910
  Dihedral  :  5.254  22.635    793
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.58 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.32), residues: 652
  helix:  None (None), residues: 0
  sheet: -0.01 (0.33), residues: 247
  loop : -1.11 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 168 
 HIS   0.002   0.001   HIS G 167 
 PHE   0.018   0.002   PHE G 160 
 TYR   0.009   0.001   TYR H  95 
 ARG   0.005   0.000   ARG I  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2605.84 seconds
wall clock time: 47 minutes 9.52 seconds (2829.52 seconds total)