Starting phenix.real_space_refine
on Sat May  2 13:56:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qqe_53299/05_2026/9qqe_53299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qqe_53299/05_2026/9qqe_53299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qqe_53299/05_2026/9qqe_53299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qqe_53299/05_2026/9qqe_53299.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qqe_53299/05_2026/9qqe_53299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qqe_53299/05_2026/9qqe_53299.map"
  }
  resolution = 2.78
  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=   0.013
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      22      5.16       5
     C    3801      2.51       5
     N    1050      2.21       5
     O    1169      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6042
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2182
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 10, 'TRANS': 257}
    Chain: "P"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 72
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
    Chain: "B"
      Number of atoms: 747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 747
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1580
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1461
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 14, 'TRANS': 180}
          Chain breaks: 1
  Time building chain proxies: 1.42, per 1000 atoms: 0.24
  Number of scatterers: 6042
  At special positions: 0
  Unit cell: (63.492, 69.19, 151.404, 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      22     16.00
     O    1169      8.00
     N    1050      7.00
     C    3801      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=1.52
    Simple disulfide: pdb=" SG  CYS H 149 " - pdb=" SG  CYS H 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 138 " - pdb=" SG  CYS L 197 " 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
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 304.8 milliseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1426

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 19 sheets defined
      15.6% alpha, 44.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.518A  pdb=" N   GLU A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN A  54 " --> pdb=" O   PRO A  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 49 through 54'
    Processing helix  chain 'A' and resid 56 through 86
    Processing helix  chain 'A' and resid 137 through 150
    Processing helix  chain 'A' and resid 151 through 162
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.535A  pdb=" N   HIS H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.912A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 195 through 201
      removed outlier: 4.369A  pdb=" N   GLY H 199 " --> pdb=" O   SER H 195 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   THR H 200 " --> pdb=" O   SER H 196 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.680A  pdb=" N   ASP L  83 " --> pdb=" O   GLN L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 125 through 131
    Processing helix  chain 'L' and resid 185 through 192
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 6.716A  pdb=" N   GLY A  26 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ALA A  24 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   CYS A 101 " --> pdb=" O   MET A   5 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TYR A  99 " --> pdb=" O   TYR A   7 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   HIS A 114 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ALA A 125 " --> pdb=" O   HIS A 114 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   TYR A 116 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 4.010A  pdb=" N   HIS A 188 " --> pdb=" O   TRP A 204 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER A 207 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   PHE A 241 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 192
      removed outlier: 4.010A  pdb=" N   HIS A 188 " --> pdb=" O   TRP A 204 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER A 207 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   PHE A 241 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216
    Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 219
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11
      removed outlier: 3.562A  pdb=" N   THR B  68 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 11
      removed outlier: 3.562A  pdb=" N   THR B  68 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER B  55 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 45
      removed outlier: 3.767A  pdb=" N   VAL B  82 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B  91 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.279A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE H 116 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 154
      removed outlier: 5.462A  pdb=" N   GLY H 148 " --> pdb=" O   VAL H 191 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   VAL H 191 " --> pdb=" O   GLY H 148 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LEU H 150 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   SER H 189 " --> pdb=" O   LEU H 150 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   LYS H 152 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU H 187 " --> pdb=" O   LYS H 152 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 154
      removed outlier: 5.462A  pdb=" N   GLY H 148 " --> pdb=" O   VAL H 191 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   VAL H 191 " --> pdb=" O   GLY H 148 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LEU H 150 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   SER H 189 " --> pdb=" O   LEU H 150 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   LYS H 152 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU H 187 " --> pdb=" O   LYS H 152 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 160 through 163
      removed outlier: 3.890A  pdb=" N   TYR H 203 " --> pdb=" O   VAL H 220 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12
      removed outlier: 3.634A  pdb=" N   ALA L  85 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12
      removed outlier: 3.634A  pdb=" N   ALA L  85 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY L  98 " --> pdb=" O   ASP L  93 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AB8, first strand: chain 'L' and resid 120 through 122
      removed outlier: 3.805A  pdb=" N   VAL L 137 " --> pdb=" O   PHE L 122 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   THR L 135 " --> pdb=" O   LEU L 184 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU L 184 " --> pdb=" O   THR L 135 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   VAL L 137 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   LEU L 182 " --> pdb=" O   VAL L 137 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LEU L 139 " --> pdb=" O   SER L 180 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   SER L 180 " --> pdb=" O   LEU L 139 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   SER L 141 " --> pdb=" O   ALA L 178 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ALA L 178 " --> pdb=" O   SER L 141 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 120 through 122
      removed outlier: 3.805A  pdb=" N   VAL L 137 " --> pdb=" O   PHE L 122 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   THR L 135 " --> pdb=" O   LEU L 184 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU L 184 " --> pdb=" O   THR L 135 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   VAL L 137 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   LEU L 182 " --> pdb=" O   VAL L 137 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LEU L 139 " --> pdb=" O   SER L 180 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   SER L 180 " --> pdb=" O   LEU L 139 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   SER L 141 " --> pdb=" O   ALA L 178 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ALA L 178 " --> pdb=" O   SER L 141 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 150 through 153

    273 hydrogen bonds defined for protein.
    696 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 993
        1.30 -     1.43: 1807
        1.43 -     1.56: 3368
        1.56 -     1.69: 1
        1.69 -     1.82: 30
  Bond restraints: 6199
  Sorted by residual:
  bond pdb=" CA  CYS A 164 "
       pdb=" C   CYS A 164 "
    ideal  model  delta    sigma   weight residual
    1.524  1.467  0.057 1.27e-02 6.20e+03 1.99e+01
  bond pdb=" C   GLY A 175 "
       pdb=" O   GLY A 175 "
    ideal  model  delta    sigma   weight residual
    1.235  1.176  0.059 1.35e-02 5.49e+03 1.91e+01
  bond pdb=" CA  GLY A 175 "
       pdb=" C   GLY A 175 "
    ideal  model  delta    sigma   weight residual
    1.514  1.458  0.056 1.41e-02 5.03e+03 1.58e+01
  bond pdb=" CA  MET H  34 "
       pdb=" C   MET H  34 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.18e-02 7.18e+03 1.32e+01
  bond pdb=" N   ARG A 202 "
       pdb=" CA  ARG A 202 "
    ideal  model  delta    sigma   weight residual
    1.455  1.498 -0.043 1.25e-02 6.40e+03 1.18e+01
  ... (remaining 6194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 7899
        2.46 -     4.91: 429
        4.91 -     7.37: 80
        7.37 -     9.83: 13
        9.83 -    12.28: 5
  Bond angle restraints: 8426
  Sorted by residual:
  angle pdb=" N   ASP A 238 "
        pdb=" CA  ASP A 238 "
        pdb=" C   ASP A 238 "
      ideal   model   delta    sigma   weight residual
     112.41  100.50   11.91 1.30e+00 5.92e-01 8.39e+01
  angle pdb=" N   ALA L 147 "
        pdb=" CA  ALA L 147 "
        pdb=" C   ALA L 147 "
      ideal   model   delta    sigma   weight residual
     110.24  121.94  -11.70 1.41e+00 5.03e-01 6.89e+01
  angle pdb=" N   GLY L 146 "
        pdb=" CA  GLY L 146 "
        pdb=" C   GLY L 146 "
      ideal   model   delta    sigma   weight residual
     111.02  123.30  -12.28 1.86e+00 2.89e-01 4.36e+01
  angle pdb=" N   MET A 138 "
        pdb=" CA  MET A 138 "
        pdb=" C   MET A 138 "
      ideal   model   delta    sigma   weight residual
     111.36  117.95   -6.59 1.09e+00 8.42e-01 3.66e+01
  angle pdb=" C   ASN L  53 "
        pdb=" CA  ASN L  53 "
        pdb=" CB  ASN L  53 "
      ideal   model   delta    sigma   weight residual
     109.80  100.90    8.90 1.61e+00 3.86e-01 3.06e+01
  ... (remaining 8421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 3289
       17.31 -    34.61: 284
       34.61 -    51.92: 72
       51.92 -    69.23: 10
       69.23 -    86.54: 5
  Dihedral angle restraints: 3660
    sinusoidal: 1434
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -13.16  -72.84     1      1.00e+01 1.00e-02 6.77e+01
  dihedral pdb=" C   TYR A 209 "
           pdb=" N   TYR A 209 "
           pdb=" CA  TYR A 209 "
           pdb=" CB  TYR A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.91   14.31     0      2.50e+00 1.60e-01 3.28e+01
  dihedral pdb=" N   TYR A 209 "
           pdb=" C   TYR A 209 "
           pdb=" CA  TYR A 209 "
           pdb=" CB  TYR A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.18  -13.38     0      2.50e+00 1.60e-01 2.86e+01
  ... (remaining 3657 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 785
       0.109 -    0.218: 89
       0.218 -    0.327: 24
       0.327 -    0.436: 4
       0.436 -    0.545: 1
  Chirality restraints: 903
  Sorted by residual:
  chirality pdb=" CA  TYR A 209 "
            pdb=" N   TYR A 209 "
            pdb=" C   TYR A 209 "
            pdb=" CB  TYR A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.42e+00
  chirality pdb=" CA  ALA L 147 "
            pdb=" N   ALA L 147 "
            pdb=" C   ALA L 147 "
            pdb=" CB  ALA L 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.12    0.37 2.00e-01 2.50e+01 3.39e+00
  chirality pdb=" CA  PRO H 132 "
            pdb=" N   PRO H 132 "
            pdb=" C   PRO H 132 "
            pdb=" CB  PRO H 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.10e+00
  ... (remaining 900 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 209 "    0.071 2.00e-02 2.50e+03   3.73e-02 2.79e+01
        pdb=" CG  TYR A 209 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 209 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 209 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 209 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 209 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 209 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 209 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 208 "    0.056 2.00e-02 2.50e+03   3.44e-02 2.07e+01
        pdb=" CG  PHE A 208 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 208 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 208 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 208 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 208 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 208 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 263 "    0.042 2.00e-02 2.50e+03   3.13e-02 1.47e+01
        pdb=" CG  HIS A 263 "   -0.047 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 263 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 263 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 263 "    0.018 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 263 "    0.028 2.00e-02 2.50e+03
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 724
        2.75 -     3.29: 5766
        3.29 -     3.82: 10425
        3.82 -     4.36: 12781
        4.36 -     4.90: 21638
  Nonbonded interactions: 51334
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L 185 "
            pdb=" OE1 GLU L 187 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" N   GLU P   8 "
            pdb=" OE1 GLU P   8 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OD2 ASP H  73 "
            pdb=" OH  TYR H  80 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   VAL H 151 "
            pdb=" OG  SER H 186 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD1 ASP A 122 "
            pdb=" NE1 TRP B  60 "
     model   vdw
     2.322 3.120
  ... (remaining 51329 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:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.510
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
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      :  0.010   0.509   6204  Z= 0.630
  Angle     :  1.330  33.122   8436  Z= 0.836
  Chirality :  0.081   0.545    903
  Planarity :  0.007   0.074   1087
  Dihedral  : 13.980  86.535   2219
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.73 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 17.38 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.14 %
  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: -0.25 (0.31), residues: 751
  helix:  0.55 (0.52), residues: 97
  sheet: -0.01 (0.32), residues: 273
  loop : -0.36 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 181 
 TYR   0.071   0.003   TYR A 209 
 PHE   0.056   0.005   PHE A 208 
 TRP   0.019   0.002   TRP A  60 
 HIS   0.011   0.002   HIS L 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00791 ( 6199)
  covalent geometry    : angle       1.27346 ( 8426)
  SS BOND              : bond        0.22751 (    5)
  SS BOND              : angle      11.19630 (   10)
  hydrogen bonds       : bond        0.21183 (  233)
  hydrogen bonds       : angle       9.65687 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   19 GLU cc_start: 0.7610 (tt0) cc_final: 0.7233 (pp20)
REVERT: A   55 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6413 (mm-30)
REVERT: A  132 SER cc_start: 0.8541 (m) cc_final: 0.8269 (p)
REVERT: A  174 ASN cc_start: 0.7716 (m-40) cc_final: 0.7467 (m110)
REVERT: A  189 MET cc_start: 0.2563 (mtp) cc_final: 0.2095 (ttt)
REVERT: B   42 ASN cc_start: 0.8683 (m-40) cc_final: 0.8423 (m-40)
REVERT: H  131 PHE cc_start: 0.7631 (m-80) cc_final: 0.7157 (m-10)
REVERT: L   16 GLN cc_start: 0.8797 (mt0) cc_final: 0.8405 (mt0)
REVERT: L  112 GLN cc_start: 0.7822 (mt0) cc_final: 0.7461 (mt0)
  outliers start: 2
  outliers final: 2
  residues processed: 130
  average time/residue: 0.5050
  time to fit residues: 68.8954
Evaluate side-chains
  89 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain B residue   70 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.152649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.120816 restraints weight = 9950.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 3.02
r_work: 0.3719 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6204  Z= 0.182
  Angle     :  0.670   7.470   8436  Z= 0.355
  Chirality :  0.047   0.251    903
  Planarity :  0.005   0.060   1087
  Dihedral  :  5.834  50.621    848
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 18.45 %
    Favored  : 76.52 %
  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: -0.18 (0.31), residues: 751
  helix:  0.12 (0.48), residues: 98
  sheet:  0.34 (0.31), residues: 286
  loop : -0.47 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 106 
 TYR   0.024   0.002   TYR L 176 
 PHE   0.039   0.002   PHE A 109 
 TRP   0.015   0.001   TRP A  60 
 HIS   0.006   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6199)
  covalent geometry    : angle       0.66625 ( 8426)
  SS BOND              : bond        0.00345 (    5)
  SS BOND              : angle       2.12463 (   10)
  hydrogen bonds       : bond        0.05125 (  233)
  hydrogen bonds       : angle       6.69533 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLU cc_start: 0.7829 (tt0) cc_final: 0.7257 (pp20)
REVERT: A  132 SER cc_start: 0.8409 (m) cc_final: 0.8179 (p)
REVERT: A  189 MET cc_start: 0.3446 (mtp) cc_final: 0.2817 (ttt)
REVERT: H   39 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8231 (mm-40)
REVERT: H  204 ILE cc_start: 0.8108 (mm) cc_final: 0.7898 (pp)
REVERT: L   16 GLN cc_start: 0.9038 (mt0) cc_final: 0.8575 (mt0)
  outliers start: 33
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4565
  time to fit residues: 52.4588
Evaluate side-chains
  89 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   70 PHE
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   19 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 26 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
B  42 ASN
L 112 GLN
L 188 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.153174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.121289 restraints weight = 9897.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 3.05
r_work: 0.3734 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6204  Z= 0.151
  Angle     :  0.611   7.510   8436  Z= 0.319
  Chirality :  0.045   0.194    903
  Planarity :  0.004   0.049   1087
  Dihedral  :  5.618  51.530    848
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 19.36 %
    Favored  : 75.30 %
  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: -0.03 (0.31), residues: 751
  helix:  0.40 (0.50), residues: 98
  sheet:  0.51 (0.32), residues: 272
  loop : -0.46 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 106 
 TYR   0.019   0.002   TYR L 176 
 PHE   0.040   0.002   PHE A 109 
 TRP   0.014   0.001   TRP A  60 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6199)
  covalent geometry    : angle       0.60997 ( 8426)
  SS BOND              : bond        0.00299 (    5)
  SS BOND              : angle       1.31098 (   10)
  hydrogen bonds       : bond        0.04197 (  233)
  hydrogen bonds       : angle       5.91368 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 88
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 GLN cc_start: 0.7130 (tt0) cc_final: 0.6597 (tm-30)
REVERT: A  222 GLU cc_start: 0.9259 (tp30) cc_final: 0.8898 (tm-30)
REVERT: B   36 GLU cc_start: 0.7125 (mp0) cc_final: 0.6703 (tt0)
REVERT: B   44 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7257 (mt-10)
REVERT: H   46 GLU cc_start: 0.8203 (tt0) cc_final: 0.7524 (tm-30)
REVERT: H   50 SER cc_start: 0.9001 (t) cc_final: 0.8652 (m)
REVERT: H   73 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7163 (p0)
REVERT: H  153 ASP cc_start: 0.7764 (m-30) cc_final: 0.7432 (t0)
REVERT: H  168 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7693 (tt)
REVERT: H  204 ILE cc_start: 0.8148 (mm) cc_final: 0.7881 (pp)
REVERT: L   16 GLN cc_start: 0.9074 (mt0) cc_final: 0.8604 (mt0)
REVERT: L  143 PHE cc_start: 0.6811 (m-80) cc_final: 0.6515 (m-10)
  outliers start: 35
  outliers final: 14
  residues processed: 106
  average time/residue: 0.4264
  time to fit residues: 47.8119
Evaluate side-chains
  99 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain B residue   44 GLU
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   70 PHE
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain L residue   18 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
H  82 GLN
L 112 GLN
L 188 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.147691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.115626 restraints weight = 10032.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 3.02
r_work: 0.3669 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6204  Z= 0.267
  Angle     :  0.695   9.431   8436  Z= 0.361
  Chirality :  0.047   0.197    903
  Planarity :  0.005   0.039   1087
  Dihedral  :  5.956  56.595    848
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 19.36 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.31), residues: 751
  helix:  0.17 (0.50), residues: 98
  sheet:  0.38 (0.32), residues: 277
  loop : -0.46 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  75 
 TYR   0.020   0.002   TYR A  99 
 PHE   0.039   0.002   PHE A 109 
 TRP   0.011   0.002   TRP A  60 
 HIS   0.007   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 6199)
  covalent geometry    : angle       0.69365 ( 8426)
  SS BOND              : bond        0.00231 (    5)
  SS BOND              : angle       1.34040 (   10)
  hydrogen bonds       : bond        0.04729 (  233)
  hydrogen bonds       : angle       5.99302 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 86
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7468 (t80) cc_final: 0.7069 (t80)
REVERT: A  180 GLN cc_start: 0.7210 (tt0) cc_final: 0.6623 (tm-30)
REVERT: A  189 MET cc_start: 0.3330 (ttt) cc_final: 0.0782 (ttt)
REVERT: A  222 GLU cc_start: 0.9319 (tp30) cc_final: 0.8959 (tm-30)
REVERT: B   36 GLU cc_start: 0.7117 (mp0) cc_final: 0.6690 (tt0)
REVERT: B   69 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6948 (mm-30)
REVERT: B   70 PHE cc_start: 0.4911 (OUTLIER) cc_final: 0.2941 (p90)
REVERT: H   46 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7646 (tm-30)
REVERT: H   73 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7275 (p0)
REVERT: H  153 ASP cc_start: 0.7869 (m-30) cc_final: 0.7473 (t0)
REVERT: H  168 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7521 (tt)
REVERT: H  204 ILE cc_start: 0.8061 (mm) cc_final: 0.7817 (pp)
REVERT: L   80 GLN cc_start: 0.6742 (mm-40) cc_final: 0.6400 (mp10)
REVERT: L   86 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6492 (m-30)
REVERT: L  106 ARG cc_start: 0.7746 (mtp85) cc_final: 0.6704 (mmp80)
  outliers start: 41
  outliers final: 16
  residues processed: 109
  average time/residue: 0.4528
  time to fit residues: 51.9583
Evaluate side-chains
  98 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    4 ASP
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   70 PHE
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   86 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
L 112 GLN
L 188 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.151106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.119256 restraints weight = 10046.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 3.07
r_work: 0.3698 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6204  Z= 0.166
  Angle     :  0.642   9.776   8436  Z= 0.329
  Chirality :  0.045   0.212    903
  Planarity :  0.004   0.038   1087
  Dihedral  :  5.734  57.472    848
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 19.97 %
    Favored  : 74.24 %
  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: -0.07 (0.31), residues: 751
  helix:  0.22 (0.51), residues: 98
  sheet:  0.47 (0.32), residues: 279
  loop : -0.44 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  62 
 TYR   0.017   0.002   TYR L 176 
 PHE   0.038   0.002   PHE L 143 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.006   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6199)
  covalent geometry    : angle       0.64009 ( 8426)
  SS BOND              : bond        0.00425 (    5)
  SS BOND              : angle       1.42009 (   10)
  hydrogen bonds       : bond        0.04074 (  233)
  hydrogen bonds       : angle       5.66911 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 85
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7475 (t80) cc_final: 0.7088 (t80)
REVERT: A  180 GLN cc_start: 0.7148 (tt0) cc_final: 0.6548 (tm-30)
REVERT: A  222 GLU cc_start: 0.9304 (tp30) cc_final: 0.9003 (tm-30)
REVERT: B   36 GLU cc_start: 0.7044 (mp0) cc_final: 0.6642 (tt0)
REVERT: B   69 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7164 (mm-30)
REVERT: H   46 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7547 (tm-30)
REVERT: H   73 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7324 (p0)
REVERT: H   89 GLU cc_start: 0.8092 (mp0) cc_final: 0.7857 (pm20)
REVERT: H  153 ASP cc_start: 0.7800 (m-30) cc_final: 0.7394 (t0)
REVERT: H  168 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7554 (tt)
REVERT: H  204 ILE cc_start: 0.8119 (mm) cc_final: 0.7879 (pp)
REVERT: L   55 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.5832 (ttm170)
REVERT: L   80 GLN cc_start: 0.6514 (mm-40) cc_final: 0.6172 (mp10)
REVERT: L   86 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6461 (m-30)
REVERT: L  106 ARG cc_start: 0.7783 (mtp85) cc_final: 0.6743 (mmp80)
  outliers start: 38
  outliers final: 21
  residues processed: 108
  average time/residue: 0.4616
  time to fit residues: 52.6236
Evaluate side-chains
  106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue    7 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   67 TYR
Chi-restraints excluded: chain B residue   70 PHE
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   86 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:    5.9990
   chunk 68 optimal weight:    0.4980
   chunk 4 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 155 GLN
A 260 HIS
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 GLN
L 188 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.147825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.115564 restraints weight = 10114.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 3.08
r_work: 0.3668 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6204  Z= 0.231
  Angle     :  0.683   9.239   8436  Z= 0.352
  Chirality :  0.046   0.191    903
  Planarity :  0.005   0.035   1087
  Dihedral  :  5.846  56.517    848
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 19.05 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.32), residues: 751
  helix:  0.55 (0.53), residues: 91
  sheet:  0.34 (0.32), residues: 279
  loop : -0.48 (0.34), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.017   0.002   TYR A  99 
 PHE   0.041   0.003   PHE L 143 
 TRP   0.012   0.001   TRP A  60 
 HIS   0.006   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 6199)
  covalent geometry    : angle       0.68256 ( 8426)
  SS BOND              : bond        0.00227 (    5)
  SS BOND              : angle       1.14809 (   10)
  hydrogen bonds       : bond        0.04399 (  233)
  hydrogen bonds       : angle       5.71460 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 83
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7525 (t80) cc_final: 0.7123 (t80)
REVERT: A  180 GLN cc_start: 0.7260 (tt0) cc_final: 0.6697 (tm-30)
REVERT: A  188 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.5864 (p-80)
REVERT: A  222 GLU cc_start: 0.9248 (tp30) cc_final: 0.8914 (pp20)
REVERT: B   36 GLU cc_start: 0.7065 (mp0) cc_final: 0.6753 (tt0)
REVERT: H   46 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7658 (tm-30)
REVERT: H   73 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7425 (p0)
REVERT: H  168 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7524 (tt)
REVERT: H  204 ILE cc_start: 0.8117 (mm) cc_final: 0.7883 (pp)
  outliers start: 47
  outliers final: 28
  residues processed: 111
  average time/residue: 0.4280
  time to fit residues: 50.4015
Evaluate side-chains
  112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue    7 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   67 TYR
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue  140 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
L 112 GLN
L 192 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.151698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.119718 restraints weight = 10054.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 3.12
r_work: 0.3737 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6204  Z= 0.148
  Angle     :  0.643   8.977   8436  Z= 0.329
  Chirality :  0.045   0.268    903
  Planarity :  0.004   0.035   1087
  Dihedral  :  5.269  32.834    846
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 21.49 %
    Favored  : 73.48 %
  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: -0.15 (0.31), residues: 751
  helix:  0.18 (0.51), residues: 98
  sheet:  0.36 (0.31), residues: 279
  loop : -0.45 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 108 
 TYR   0.017   0.002   TYR L 176 
 PHE   0.023   0.002   PHE A 109 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.006   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6199)
  covalent geometry    : angle       0.64286 ( 8426)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       0.87569 (   10)
  hydrogen bonds       : bond        0.03811 (  233)
  hydrogen bonds       : angle       5.43600 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 89
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7514 (t80) cc_final: 0.7161 (t80)
REVERT: A  180 GLN cc_start: 0.7171 (tt0) cc_final: 0.6527 (tm-30)
REVERT: A  222 GLU cc_start: 0.9282 (tp30) cc_final: 0.8947 (pp20)
REVERT: B   36 GLU cc_start: 0.6943 (mp0) cc_final: 0.6580 (tt0)
REVERT: B   42 ASN cc_start: 0.8568 (m110) cc_final: 0.8269 (m-40)
REVERT: H   46 GLU cc_start: 0.8267 (tt0) cc_final: 0.7574 (tm-30)
REVERT: H   73 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7352 (p0)
REVERT: H  153 ASP cc_start: 0.7855 (m-30) cc_final: 0.7525 (t0)
REVERT: H  168 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7463 (tt)
REVERT: H  204 ILE cc_start: 0.8069 (mm) cc_final: 0.7868 (pp)
REVERT: L   80 GLN cc_start: 0.6369 (mm-40) cc_final: 0.6045 (mp10)
  outliers start: 33
  outliers final: 24
  residues processed: 108
  average time/residue: 0.4196
  time to fit residues: 48.0599
Evaluate side-chains
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue    7 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   67 TYR
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue  135 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0770
   chunk 67 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
B  24 ASN
B  89 GLN
L 112 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.150583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.118584 restraints weight = 9972.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 3.09
r_work: 0.3719 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6204  Z= 0.178
  Angle     :  0.658   9.710   8436  Z= 0.337
  Chirality :  0.045   0.182    903
  Planarity :  0.004   0.035   1087
  Dihedral  :  5.276  31.958    846
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 21.80 %
    Favored  : 72.71 %
  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: -0.10 (0.31), residues: 751
  helix:  0.12 (0.51), residues: 98
  sheet:  0.42 (0.32), residues: 279
  loop : -0.41 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 108 
 TYR   0.013   0.002   TYR L 176 
 PHE   0.016   0.002   PHE L 143 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6199)
  covalent geometry    : angle       0.65793 ( 8426)
  SS BOND              : bond        0.00209 (    5)
  SS BOND              : angle       0.89668 (   10)
  hydrogen bonds       : bond        0.03921 (  233)
  hydrogen bonds       : angle       5.42821 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 86
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7527 (t80) cc_final: 0.7171 (t80)
REVERT: A  116 TYR cc_start: 0.7856 (t80) cc_final: 0.7383 (t80)
REVERT: A  180 GLN cc_start: 0.7239 (tt0) cc_final: 0.6584 (tm-30)
REVERT: A  189 MET cc_start: 0.3309 (ttt) cc_final: 0.3079 (tpt)
REVERT: A  222 GLU cc_start: 0.9235 (tp30) cc_final: 0.8949 (pp20)
REVERT: B   36 GLU cc_start: 0.6987 (mp0) cc_final: 0.6710 (tt0)
REVERT: B   42 ASN cc_start: 0.8512 (m110) cc_final: 0.8258 (m-40)
REVERT: H   46 GLU cc_start: 0.8267 (tt0) cc_final: 0.7652 (tm-30)
REVERT: H   73 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7449 (p0)
REVERT: H  153 ASP cc_start: 0.7819 (m-30) cc_final: 0.7464 (t0)
REVERT: H  168 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7515 (tt)
REVERT: H  204 ILE cc_start: 0.8116 (mm) cc_final: 0.7904 (pp)
REVERT: L   16 GLN cc_start: 0.9109 (mt0) cc_final: 0.8676 (mt0)
  outliers start: 36
  outliers final: 24
  residues processed: 109
  average time/residue: 0.4056
  time to fit residues: 46.9178
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue    7 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue  135 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.1980
   chunk 47 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
B  24 ASN
L 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.152447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.120908 restraints weight = 9929.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 3.06
r_work: 0.3725 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6204  Z= 0.157
  Angle     :  0.669  11.944   8436  Z= 0.343
  Chirality :  0.045   0.224    903
  Planarity :  0.004   0.034   1087
  Dihedral  :  5.223  32.111    846
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.63 %
    Favored  : 72.10 %
  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: -0.06 (0.32), residues: 751
  helix:  0.13 (0.51), residues: 98
  sheet:  0.46 (0.32), residues: 279
  loop : -0.39 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 108 
 TYR   0.036   0.002   TYR H 185 
 PHE   0.022   0.002   PHE B  70 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6199)
  covalent geometry    : angle       0.66906 ( 8426)
  SS BOND              : bond        0.00230 (    5)
  SS BOND              : angle       0.85921 (   10)
  hydrogen bonds       : bond        0.03803 (  233)
  hydrogen bonds       : angle       5.35718 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7514 (t80) cc_final: 0.7166 (t80)
REVERT: A  180 GLN cc_start: 0.7152 (tt0) cc_final: 0.6580 (tm-30)
REVERT: A  189 MET cc_start: 0.3375 (OUTLIER) cc_final: 0.3129 (tpt)
REVERT: A  222 GLU cc_start: 0.9281 (tp30) cc_final: 0.8916 (pp20)
REVERT: B   36 GLU cc_start: 0.6897 (mp0) cc_final: 0.6552 (tt0)
REVERT: B   41 LYS cc_start: 0.7755 (ptmm) cc_final: 0.7246 (tmtt)
REVERT: B   42 ASN cc_start: 0.8523 (m110) cc_final: 0.7838 (m-40)
REVERT: H   46 GLU cc_start: 0.8240 (tt0) cc_final: 0.7493 (tm-30)
REVERT: H   73 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7370 (p0)
REVERT: H  153 ASP cc_start: 0.7837 (m-30) cc_final: 0.7510 (t0)
REVERT: H  168 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (tt)
REVERT: H  204 ILE cc_start: 0.8090 (mm) cc_final: 0.7881 (pp)
REVERT: L   16 GLN cc_start: 0.9072 (mt0) cc_final: 0.8633 (mt0)
  outliers start: 28
  outliers final: 23
  residues processed: 103
  average time/residue: 0.4208
  time to fit residues: 46.0187
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain P residue    7 LEU
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue  135 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 52 optimal weight:    0.0070
   chunk 7 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 53 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
B  24 ASN
L 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.153504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.122026 restraints weight = 10032.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 3.10
r_work: 0.3752 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6204  Z= 0.145
  Angle     :  0.662   8.706   8436  Z= 0.342
  Chirality :  0.045   0.179    903
  Planarity :  0.004   0.034   1087
  Dihedral  :  5.092  32.026    846
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.39 %
    Favored  : 71.49 %
  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:  0.06 (0.32), residues: 751
  helix:  0.23 (0.52), residues: 98
  sheet:  0.53 (0.32), residues: 279
  loop : -0.30 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 108 
 TYR   0.021   0.002   TYR H 185 
 PHE   0.011   0.002   PHE L 143 
 TRP   0.014   0.001   TRP A  60 
 HIS   0.006   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6199)
  covalent geometry    : angle       0.66162 ( 8426)
  SS BOND              : bond        0.00228 (    5)
  SS BOND              : angle       0.86036 (   10)
  hydrogen bonds       : bond        0.03656 (  233)
  hydrogen bonds       : angle       5.25360 (  696)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7505 (t80) cc_final: 0.7148 (t80)
REVERT: A  180 GLN cc_start: 0.7120 (tt0) cc_final: 0.6529 (tm-30)
REVERT: A  189 MET cc_start: 0.3335 (OUTLIER) cc_final: 0.3100 (tpt)
REVERT: A  222 GLU cc_start: 0.9272 (tp30) cc_final: 0.8912 (pp20)
REVERT: B   36 GLU cc_start: 0.6904 (mp0) cc_final: 0.6551 (tt0)
REVERT: B   41 LYS cc_start: 0.7716 (ptmm) cc_final: 0.7149 (tmtt)
REVERT: B   42 ASN cc_start: 0.8439 (m110) cc_final: 0.7200 (m-40)
REVERT: B   44 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7171 (mp0)
REVERT: B   59 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7584 (p0)
REVERT: H   46 GLU cc_start: 0.8178 (tt0) cc_final: 0.7511 (tm-30)
REVERT: H   73 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7339 (p0)
REVERT: H  153 ASP cc_start: 0.7790 (m-30) cc_final: 0.6967 (t70)
REVERT: H  168 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7475 (tt)
REVERT: L   16 GLN cc_start: 0.9064 (mt0) cc_final: 0.8653 (mt0)
  outliers start: 27
  outliers final: 20
  residues processed: 102
  average time/residue: 0.4534
  time to fit residues: 48.8547
Evaluate side-chains
  105 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 MET
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain P residue    6 LEU
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain H residue  168 LEU
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain H residue  192 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue  135 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0070
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
B  24 ASN
L 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.153630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.121998 restraints weight = 10009.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 3.10
r_work: 0.3748 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6204  Z= 0.155
  Angle     :  0.681  12.390   8436  Z= 0.349
  Chirality :  0.045   0.167    903
  Planarity :  0.004   0.042   1087
  Dihedral  :  4.878  30.606    842
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.93 %
    Favored  : 71.34 %
  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:  0.11 (0.32), residues: 751
  helix:  0.22 (0.52), residues: 98
  sheet:  0.55 (0.32), residues: 279
  loop : -0.25 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG L  62 
 TYR   0.029   0.002   TYR H 185 
 PHE   0.012   0.002   PHE B  70 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6199)
  covalent geometry    : angle       0.68015 ( 8426)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.92801 (   10)
  hydrogen bonds       : bond        0.03737 (  233)
  hydrogen bonds       : angle       5.22288 (  696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2394.53 seconds
wall clock time: 41 minutes 37.39 seconds (2497.39 seconds total)