Starting phenix.real_space_refine
on Sat May  2 16:06:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/20yc_67392/05_2026/20yc_67392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/20yc_67392/05_2026/20yc_67392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/20yc_67392/05_2026/20yc_67392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/20yc_67392/05_2026/20yc_67392.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/20yc_67392/05_2026/20yc_67392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/20yc_67392/05_2026/20yc_67392.map"
  }
  resolution = 3.4
  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=   0.002 sd=   0.030
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      58      5.16       5
     C    4540      2.51       5
     N    1196      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 7082
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1753
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 49
    Chain: "R"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2337
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2585
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
  Time building chain proxies: 1.95, per 1000 atoms: 0.28
  Number of scatterers: 7082
  At special positions: 0
  Unit cell: (77.19, 115.32, 117.18, 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      58     16.00
     O    1288      8.00
     N    1196      7.00
     C    4540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  91 " - pdb=" SG  CYS R 168 " distance=2.05

  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: 0.61
  Conformation dependent library (CDL) restraints added in 452.4 milliseconds
  

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      49.2% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 4.066A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.261A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.892A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.114A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.703A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.666A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.725A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 352
      removed outlier: 3.583A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 20 through 51
      removed outlier: 4.625A  pdb=" N   VAL R  31 " --> pdb=" O   THR R  27 " (cutoff:3.500A)
      Proline residue:  R  32  - end of helix
      removed outlier: 3.972A  pdb=" N   GLY R  46 " --> pdb=" O   TRP R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 71
      removed outlier: 3.762A  pdb=" N   ILE R  59 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN R  60 " --> pdb=" O   ILE R  56 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   LEU R  61 " --> pdb=" O   PHE R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 71 through 82
      removed outlier: 4.465A  pdb=" N   ARG R  75 " --> pdb=" O   SER R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 122
      removed outlier: 4.034A  pdb=" N   PHE R  95 " --> pdb=" O   CYS R  91 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   TYR R 122 " --> pdb=" O   TRP R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 150
    Processing helix  chain 'R' and resid 150 through 157
    Processing helix  chain 'R' and resid 161 through 165
    Processing helix  chain 'R' and resid 168 through 172
    Processing helix  chain 'R' and resid 178 through 194
    Processing helix  chain 'R' and resid 194 through 215
      removed outlier: 3.975A  pdb=" N   ASP R 214 " --> pdb=" O   LEU R 210 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   LYS R 215 " --> pdb=" O   SER R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 222
      removed outlier: 3.719A  pdb=" N   LEU R 222 " --> pdb=" O   MET R 218 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 222 through 258
      removed outlier: 4.599A  pdb=" N   GLN R 226 " --> pdb=" O   LEU R 222 " (cutoff:3.500A)
      Proline residue:  R 245  - end of helix
      Proline residue:  R 251  - end of helix
    Processing helix  chain 'R' and resid 263 through 293
      removed outlier: 4.033A  pdb=" N   ASN R 284 " --> pdb=" O   LEU R 280 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   SER R 285 " --> pdb=" O   ALA R 281 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   CYS R 286 " --> pdb=" O   SER R 282 " (cutoff:3.500A)
      Proline residue:  R 289  - end of helix
    Processing helix  chain 'R' and resid 296 through 303
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 22
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.528A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.552A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.593A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.624A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.579A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.726A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.053A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.457A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.892A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2260
        1.34 -     1.48: 1836
        1.48 -     1.61: 3052
        1.61 -     1.74: 0
        1.74 -     1.88: 82
  Bond restraints: 7230
  Sorted by residual:
  bond pdb=" CA  ARG R  75 "
       pdb=" C   ARG R  75 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.26e-02 6.30e+03 2.16e+01
  bond pdb=" CA  THR B  47 "
       pdb=" C   THR B  47 "
    ideal  model  delta    sigma   weight residual
    1.524  1.469  0.055 1.26e-02 6.30e+03 1.89e+01
  bond pdb=" CA  HIS A 188 "
       pdb=" C   HIS A 188 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 1.24e-02 6.50e+03 1.84e+01
  bond pdb=" C   LYS R  98 "
       pdb=" N   TYR R  99 "
    ideal  model  delta    sigma   weight residual
    1.334  1.273  0.061 1.43e-02 4.89e+03 1.82e+01
  bond pdb=" C   ARG R  75 "
       pdb=" N   ILE R  76 "
    ideal  model  delta    sigma   weight residual
    1.334  1.286  0.049 1.25e-02 6.40e+03 1.52e+01
  ... (remaining 7225 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.11: 9752
        4.11 -     8.23: 38
        8.23 -    12.34: 0
       12.34 -    16.45: 0
       16.45 -    20.57: 1
  Bond angle restraints: 9791
  Sorted by residual:
  angle pdb=" CA  CYS R 168 "
        pdb=" CB  CYS R 168 "
        pdb=" SG  CYS R 168 "
      ideal   model   delta    sigma   weight residual
     114.40  134.97  -20.57 2.30e+00 1.89e-01 8.00e+01
  angle pdb=" N   THR A 324 "
        pdb=" CA  THR A 324 "
        pdb=" C   THR A 324 "
      ideal   model   delta    sigma   weight residual
     111.24  118.55   -7.31 1.38e+00 5.25e-01 2.80e+01
  angle pdb=" C   ILE R 145 "
        pdb=" CA  ILE R 145 "
        pdb=" CB  ILE R 145 "
      ideal   model   delta    sigma   weight residual
     111.97  105.45    6.52 1.28e+00 6.10e-01 2.60e+01
  angle pdb=" N   LEU R 172 "
        pdb=" CA  LEU R 172 "
        pdb=" C   LEU R 172 "
      ideal   model   delta    sigma   weight residual
     109.93  104.39    5.54 1.24e+00 6.50e-01 1.99e+01
  angle pdb=" N   TRP B 211 "
        pdb=" CA  TRP B 211 "
        pdb=" C   TRP B 211 "
      ideal   model   delta    sigma   weight residual
     108.90  115.70   -6.80 1.63e+00 3.76e-01 1.74e+01
  ... (remaining 9786 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.11: 3829
       14.11 -    28.21: 322
       28.21 -    42.32: 104
       42.32 -    56.43: 31
       56.43 -    70.54: 9
  Dihedral angle restraints: 4295
    sinusoidal: 1661
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CB  CYS R  91 "
           pdb=" SG  CYS R  91 "
           pdb=" SG  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.89  -61.89     1      1.00e+01 1.00e-02 5.08e+01
  dihedral pdb=" CA  ILE R  29 "
           pdb=" C   ILE R  29 "
           pdb=" N   LEU R  30 "
           pdb=" CA  LEU R  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.86  -21.14     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" C   HIS A 188 "
           pdb=" N   HIS A 188 "
           pdb=" CA  HIS A 188 "
           pdb=" CB  HIS A 188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.01   -9.59     0      2.50e+00 1.60e-01 1.47e+01
  ... (remaining 4292 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 989
       0.068 -    0.136: 123
       0.136 -    0.204: 5
       0.204 -    0.272: 0
       0.272 -    0.340: 2
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" CA  TYR R  99 "
            pdb=" N   TYR R  99 "
            pdb=" C   TYR R  99 "
            pdb=" CB  TYR R  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CA  CYS R 168 "
            pdb=" N   CYS R 168 "
            pdb=" C   CYS R 168 "
            pdb=" CB  CYS R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  THR A 324 "
            pdb=" N   THR A 324 "
            pdb=" C   THR A 324 "
            pdb=" CB  THR A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 1116 not shown)

  Planarity restraints: 1231
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 167 "   -0.017 2.00e-02 2.50e+03   3.54e-02 1.26e+01
        pdb=" C   LYS R 167 "    0.061 2.00e-02 2.50e+03
        pdb=" O   LYS R 167 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   CYS R 168 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  74 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.77e+00
        pdb=" C   LEU R  74 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LEU R  74 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG R  75 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 187 "    0.013 2.00e-02 2.50e+03   2.53e-02 6.42e+00
        pdb=" C   THR A 187 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   THR A 187 "    0.016 2.00e-02 2.50e+03
        pdb=" N   HIS A 188 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1228 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1373
        2.76 -     3.30: 7177
        3.30 -     3.83: 11809
        3.83 -     4.37: 14057
        4.37 -     4.90: 23593
  Nonbonded interactions: 58009
  Sorted by model distance:
  nonbonded pdb=" O   ILE R 291 "
            pdb=" OG  SER R 295 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLN R  68 "
            pdb=" OG  SER R  71 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" NH1 ARG B 251 "
            pdb=" OE2 GLU B 260 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.358 3.040
  ... (remaining 58004 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:             0.850
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.690
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
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      :  0.006   0.070   7231  Z= 0.377
  Angle     :  0.823  26.941   9793  Z= 0.495
  Chirality :  0.046   0.340   1119
  Planarity :  0.005   0.041   1231
  Dihedral  : 12.806  70.536   2586
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.15 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.57 %
    Favored  : 86.52 %
  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:  0.24 (0.28), residues: 889
  helix:  1.33 (0.26), residues: 391
  sheet:  0.05 (0.36), residues: 183
  loop : -1.23 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 175 
 TYR   0.017   0.001   TYR A 287 
 PHE   0.018   0.002   PHE A 196 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 ( 7230)
  covalent geometry    : angle       0.77439 ( 9791)
  SS BOND              : bond        0.01715 (    1)
  SS BOND              : angle      19.41709 (    2)
  hydrogen bonds       : bond        0.11628 (  387)
  hydrogen bonds       : angle       5.94592 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 212
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.6740 (tt) cc_final: 0.6535 (tt)
REVERT: A   53 MET cc_start: 0.6447 (mmt) cc_final: 0.6070 (mmt)
REVERT: A  197 LYS cc_start: 0.7063 (mttt) cc_final: 0.6359 (mttt)
REVERT: A  199 PHE cc_start: 0.7535 (m-80) cc_final: 0.7210 (m-10)
REVERT: A  240 MET cc_start: 0.6680 (tpt) cc_final: 0.6241 (tpt)
REVERT: A  250 PHE cc_start: 0.7678 (t80) cc_final: 0.7156 (t80)
REVERT: A  271 LYS cc_start: 0.7815 (pttp) cc_final: 0.7520 (pttp)
REVERT: A  277 LYS cc_start: 0.6515 (mttm) cc_final: 0.6162 (mttm)
REVERT: A  302 TYR cc_start: 0.5776 (t80) cc_final: 0.5271 (t80)
REVERT: A  310 LEU cc_start: 0.7932 (mt) cc_final: 0.7481 (mt)
REVERT: A  322 HIS cc_start: 0.6924 (t70) cc_final: 0.6293 (t70)
REVERT: R   29 ILE cc_start: 0.7481 (mt) cc_final: 0.7278 (mt)
REVERT: R   95 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.6038 (m-80)
REVERT: R  127 HIS cc_start: 0.6134 (p-80) cc_final: 0.5877 (p-80)
REVERT: R  181 GLN cc_start: 0.6765 (mm110) cc_final: 0.6160 (pp30)
REVERT: B   38 ASP cc_start: 0.7212 (m-30) cc_final: 0.6942 (m-30)
REVERT: B   96 ARG cc_start: 0.6733 (mtt180) cc_final: 0.6527 (mtt90)
REVERT: B  134 ARG cc_start: 0.6168 (ptp-110) cc_final: 0.5756 (mtm110)
REVERT: B  155 ASN cc_start: 0.7602 (m-40) cc_final: 0.7270 (m-40)
REVERT: B  191 SER cc_start: 0.8281 (t) cc_final: 0.7875 (p)
REVERT: B  277 SER cc_start: 0.8035 (t) cc_final: 0.7512 (p)
REVERT: B  280 LYS cc_start: 0.7367 (tttt) cc_final: 0.7114 (mttm)
REVERT: B  298 ASP cc_start: 0.7915 (t0) cc_final: 0.7263 (t0)
REVERT: B  325 MET cc_start: 0.6007 (tpp) cc_final: 0.5416 (tpp)
REVERT: C   21 MET cc_start: 0.7195 (mtm) cc_final: 0.6771 (mtm)
REVERT: C   47 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6693 (mt-10)
  outliers start: 7
  outliers final: 2
  residues processed: 218
  average time/residue: 0.0990
  time to fit residues: 28.0371
Evaluate side-chains
  201 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 198
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   42 TRP
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain B residue  123 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN
R 176 ASN
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.176930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.157114 restraints weight = 11837.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 3.48
r_work: 0.3922 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6537
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7231  Z= 0.139
  Angle     :  0.581   9.787   9793  Z= 0.305
  Chirality :  0.042   0.147   1119
  Planarity :  0.004   0.043   1231
  Dihedral  :  5.124  56.676    979
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.26 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.88 %
    Favored  : 80.76 %
  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:  0.88 (0.29), residues: 889
  helix:  1.89 (0.27), residues: 400
  sheet:  0.49 (0.38), residues: 169
  loop : -1.06 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  75 
 TYR   0.021   0.001   TYR R  79 
 PHE   0.013   0.001   PHE R 119 
 TRP   0.019   0.002   TRP R 142 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7230)
  covalent geometry    : angle       0.57847 ( 9791)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       3.70203 (    2)
  hydrogen bonds       : bond        0.04329 (  387)
  hydrogen bonds       : angle       4.72149 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6860 (mmt) cc_final: 0.6464 (mmt)
REVERT: A  186 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5751 (tm-30)
REVERT: A  187 THR cc_start: 0.7251 (m) cc_final: 0.6735 (m)
REVERT: A  197 LYS cc_start: 0.7161 (mttt) cc_final: 0.6575 (mttt)
REVERT: A  199 PHE cc_start: 0.7752 (m-80) cc_final: 0.7504 (m-10)
REVERT: A  240 MET cc_start: 0.6744 (tpt) cc_final: 0.6188 (tpt)
REVERT: A  250 PHE cc_start: 0.7627 (t80) cc_final: 0.7112 (t80)
REVERT: A  271 LYS cc_start: 0.7816 (pttp) cc_final: 0.7530 (pttp)
REVERT: A  277 LYS cc_start: 0.6542 (mttm) cc_final: 0.6150 (mttm)
REVERT: A  302 TYR cc_start: 0.6176 (t80) cc_final: 0.5637 (t80)
REVERT: A  310 LEU cc_start: 0.7970 (mt) cc_final: 0.7679 (mt)
REVERT: A  322 HIS cc_start: 0.7480 (t70) cc_final: 0.6758 (t70)
REVERT: R   29 ILE cc_start: 0.7570 (mt) cc_final: 0.7354 (mt)
REVERT: R   95 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5789 (m-80)
REVERT: R  121 MET cc_start: 0.6746 (mmm) cc_final: 0.6502 (mmm)
REVERT: R  127 HIS cc_start: 0.7240 (p-80) cc_final: 0.6841 (p-80)
REVERT: R  142 TRP cc_start: 0.7944 (m100) cc_final: 0.7735 (m100)
REVERT: R  151 LEU cc_start: 0.6475 (tp) cc_final: 0.5914 (tp)
REVERT: R  177 VAL cc_start: 0.7842 (m) cc_final: 0.7588 (m)
REVERT: R  181 GLN cc_start: 0.6131 (mm110) cc_final: 0.5887 (pp30)
REVERT: R  235 CYS cc_start: 0.8366 (t) cc_final: 0.8146 (t)
REVERT: R  265 LEU cc_start: 0.5608 (pt) cc_final: 0.4945 (mp)
REVERT: R  268 ARG cc_start: 0.5353 (ttp-110) cc_final: 0.4791 (ttp-170)
REVERT: R  271 LEU cc_start: 0.7633 (mt) cc_final: 0.7375 (mt)
REVERT: B   52 ARG cc_start: 0.7348 (mtt-85) cc_final: 0.7067 (ptp90)
REVERT: B   96 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7268 (mtt180)
REVERT: B  134 ARG cc_start: 0.6686 (ptp-110) cc_final: 0.6419 (mtm110)
REVERT: B  155 ASN cc_start: 0.7914 (m-40) cc_final: 0.7599 (m-40)
REVERT: B  175 GLN cc_start: 0.7297 (mm110) cc_final: 0.6804 (mm110)
REVERT: B  298 ASP cc_start: 0.8089 (t0) cc_final: 0.7818 (t0)
REVERT: B  325 MET cc_start: 0.6781 (tpp) cc_final: 0.6138 (tpp)
REVERT: B  340 ASN cc_start: 0.8034 (m-40) cc_final: 0.7493 (t0)
REVERT: C   21 MET cc_start: 0.7129 (mtm) cc_final: 0.6655 (mtm)
REVERT: C   44 HIS cc_start: 0.6914 (m90) cc_final: 0.6540 (m90)
REVERT: C   47 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6312 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 231
  average time/residue: 0.0863
  time to fit residues: 26.3747
Evaluate side-chains
  233 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0870
   chunk 53 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0270
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
B  75 GLN
B  88 ASN
B 142 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.177852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.158216 restraints weight = 11903.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.46
r_work: 0.3934 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7231  Z= 0.115
  Angle     :  0.537   7.751   9793  Z= 0.282
  Chirality :  0.042   0.195   1119
  Planarity :  0.003   0.049   1231
  Dihedral  :  4.636  53.257    977
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.92 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.46 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.29), residues: 889
  helix:  2.11 (0.27), residues: 398
  sheet:  0.44 (0.38), residues: 174
  loop : -0.92 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.016   0.001   TYR R  79 
 PHE   0.012   0.001   PHE B 253 
 TRP   0.014   0.001   TRP B 297 
 HIS   0.006   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7230)
  covalent geometry    : angle       0.53659 ( 9791)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       2.14633 (    2)
  hydrogen bonds       : bond        0.03909 (  387)
  hydrogen bonds       : angle       4.44011 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 229
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4386 (mmm160) cc_final: 0.3856 (mmm160)
REVERT: A   35 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6877 (mmtp)
REVERT: A   36 LEU cc_start: 0.7880 (mt) cc_final: 0.7670 (mt)
REVERT: A   53 MET cc_start: 0.6878 (mmt) cc_final: 0.6454 (mmt)
REVERT: A  186 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5755 (tm-30)
REVERT: A  187 THR cc_start: 0.7234 (m) cc_final: 0.6737 (m)
REVERT: A  197 LYS cc_start: 0.7194 (mttt) cc_final: 0.6588 (mttt)
REVERT: A  199 PHE cc_start: 0.7676 (m-80) cc_final: 0.7415 (m-10)
REVERT: A  240 MET cc_start: 0.6775 (tpt) cc_final: 0.6212 (tpt)
REVERT: A  250 PHE cc_start: 0.7640 (t80) cc_final: 0.7273 (t80)
REVERT: A  258 TRP cc_start: 0.8311 (m100) cc_final: 0.7725 (m100)
REVERT: A  271 LYS cc_start: 0.7696 (pttp) cc_final: 0.7412 (pttp)
REVERT: A  277 LYS cc_start: 0.6542 (mttm) cc_final: 0.6140 (mttm)
REVERT: A  302 TYR cc_start: 0.6176 (t80) cc_final: 0.5683 (t80)
REVERT: A  322 HIS cc_start: 0.7472 (t70) cc_final: 0.6808 (t70)
REVERT: A  342 VAL cc_start: 0.7416 (t) cc_final: 0.7102 (m)
REVERT: R   29 ILE cc_start: 0.7535 (mt) cc_final: 0.7309 (mt)
REVERT: R   95 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5630 (m-80)
REVERT: R  121 MET cc_start: 0.6697 (mmm) cc_final: 0.6459 (mmm)
REVERT: R  127 HIS cc_start: 0.7291 (p-80) cc_final: 0.6894 (p-80)
REVERT: R  151 LEU cc_start: 0.6354 (tp) cc_final: 0.5870 (tp)
REVERT: R  177 VAL cc_start: 0.7785 (m) cc_final: 0.7548 (m)
REVERT: R  181 GLN cc_start: 0.6175 (mm110) cc_final: 0.5914 (pp30)
REVERT: R  212 LEU cc_start: 0.8121 (mt) cc_final: 0.7806 (mt)
REVERT: R  265 LEU cc_start: 0.5660 (pt) cc_final: 0.5000 (mp)
REVERT: R  268 ARG cc_start: 0.5225 (ttp-110) cc_final: 0.4717 (ttp-170)
REVERT: B   96 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7231 (mtt180)
REVERT: B  134 ARG cc_start: 0.6645 (ptp-110) cc_final: 0.6286 (mtm110)
REVERT: B  155 ASN cc_start: 0.7940 (m-40) cc_final: 0.7629 (m-40)
REVERT: B  175 GLN cc_start: 0.7290 (mm110) cc_final: 0.6776 (mm110)
REVERT: B  220 GLN cc_start: 0.7562 (mt0) cc_final: 0.7171 (mt0)
REVERT: B  280 LYS cc_start: 0.7538 (tttm) cc_final: 0.7296 (mttm)
REVERT: B  284 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6546 (mp)
REVERT: B  290 ASP cc_start: 0.7168 (m-30) cc_final: 0.6315 (m-30)
REVERT: B  298 ASP cc_start: 0.8130 (t0) cc_final: 0.7838 (t0)
REVERT: B  325 MET cc_start: 0.6750 (tpp) cc_final: 0.6020 (tpp)
REVERT: B  340 ASN cc_start: 0.8083 (m-40) cc_final: 0.7563 (t0)
REVERT: C   21 MET cc_start: 0.7204 (mtm) cc_final: 0.6727 (mtm)
REVERT: C   44 HIS cc_start: 0.6980 (m90) cc_final: 0.6576 (m90)
REVERT: C   47 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6449 (mt-10)
  outliers start: 26
  outliers final: 11
  residues processed: 236
  average time/residue: 0.0930
  time to fit residues: 28.7970
Evaluate side-chains
  231 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 216
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0770
   chunk 82 optimal weight:    0.4980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
R 176 ASN
** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 142 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.178706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.158976 restraints weight = 11967.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 3.49
r_work: 0.3935 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7231  Z= 0.117
  Angle     :  0.544   7.006   9793  Z= 0.280
  Chirality :  0.041   0.144   1119
  Planarity :  0.003   0.050   1231
  Dihedral  :  4.536  53.316    977
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.60 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.72 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.29), residues: 889
  helix:  2.16 (0.27), residues: 398
  sheet:  0.62 (0.38), residues: 171
  loop : -0.89 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 314 
 TYR   0.012   0.001   TYR R  79 
 PHE   0.018   0.001   PHE R 299 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7230)
  covalent geometry    : angle       0.54366 ( 9791)
  SS BOND              : bond        0.00112 (    1)
  SS BOND              : angle       1.61368 (    2)
  hydrogen bonds       : bond        0.03828 (  387)
  hydrogen bonds       : angle       4.39115 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4390 (mmm160) cc_final: 0.3665 (mmm160)
REVERT: A   35 LYS cc_start: 0.7223 (mttp) cc_final: 0.6777 (mmtp)
REVERT: A   53 MET cc_start: 0.6885 (mmt) cc_final: 0.6461 (mmt)
REVERT: A  186 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5721 (tm-30)
REVERT: A  197 LYS cc_start: 0.7213 (mttt) cc_final: 0.6565 (mttt)
REVERT: A  198 MET cc_start: 0.7181 (ttt) cc_final: 0.6556 (ttm)
REVERT: A  199 PHE cc_start: 0.7664 (m-80) cc_final: 0.7385 (m-10)
REVERT: A  214 CYS cc_start: 0.7768 (m) cc_final: 0.7559 (m)
REVERT: A  240 MET cc_start: 0.6718 (tpt) cc_final: 0.6164 (tpt)
REVERT: A  250 PHE cc_start: 0.7637 (t80) cc_final: 0.7245 (t80)
REVERT: A  258 TRP cc_start: 0.8268 (m100) cc_final: 0.7701 (m100)
REVERT: A  271 LYS cc_start: 0.7684 (pttp) cc_final: 0.7396 (pttp)
REVERT: A  277 LYS cc_start: 0.6545 (mttm) cc_final: 0.6145 (mttm)
REVERT: A  302 TYR cc_start: 0.6187 (t80) cc_final: 0.5699 (t80)
REVERT: A  322 HIS cc_start: 0.7515 (t70) cc_final: 0.6832 (t70)
REVERT: A  342 VAL cc_start: 0.7446 (t) cc_final: 0.7138 (m)
REVERT: A  348 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6765 (tp)
REVERT: R   29 ILE cc_start: 0.7574 (mt) cc_final: 0.7330 (mt)
REVERT: R   95 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5684 (m-80)
REVERT: R  121 MET cc_start: 0.6709 (mmm) cc_final: 0.6446 (mmm)
REVERT: R  127 HIS cc_start: 0.7302 (p-80) cc_final: 0.6935 (p-80)
REVERT: R  151 LEU cc_start: 0.6325 (tp) cc_final: 0.5755 (tp)
REVERT: R  154 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7058 (mm)
REVERT: R  177 VAL cc_start: 0.7765 (m) cc_final: 0.7539 (m)
REVERT: R  181 GLN cc_start: 0.6338 (mm110) cc_final: 0.6046 (pp30)
REVERT: R  235 CYS cc_start: 0.8422 (t) cc_final: 0.8110 (t)
REVERT: R  242 CYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7455 (t)
REVERT: R  268 ARG cc_start: 0.5254 (ttp-110) cc_final: 0.4761 (ttp-170)
REVERT: B   96 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7185 (mtt90)
REVERT: B  134 ARG cc_start: 0.6642 (ptp-110) cc_final: 0.6307 (mtm110)
REVERT: B  155 ASN cc_start: 0.7914 (m-40) cc_final: 0.7583 (m-40)
REVERT: B  175 GLN cc_start: 0.7384 (mm110) cc_final: 0.6862 (mm110)
REVERT: B  191 SER cc_start: 0.8407 (t) cc_final: 0.8173 (p)
REVERT: B  217 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6819 (tmm)
REVERT: B  220 GLN cc_start: 0.7562 (mt0) cc_final: 0.7178 (mt0)
REVERT: B  277 SER cc_start: 0.8149 (t) cc_final: 0.7417 (p)
REVERT: B  280 LYS cc_start: 0.7458 (tttm) cc_final: 0.7220 (mttm)
REVERT: B  284 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6528 (mp)
REVERT: B  298 ASP cc_start: 0.8115 (t0) cc_final: 0.7833 (t0)
REVERT: B  315 VAL cc_start: 0.7736 (p) cc_final: 0.7408 (m)
REVERT: B  325 MET cc_start: 0.6759 (tpp) cc_final: 0.5998 (tpp)
REVERT: B  340 ASN cc_start: 0.8155 (m-40) cc_final: 0.7735 (t0)
REVERT: C   21 MET cc_start: 0.7216 (mtm) cc_final: 0.6711 (mtm)
REVERT: C   44 HIS cc_start: 0.6994 (m90) cc_final: 0.6643 (m90)
REVERT: C   47 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6451 (mt-10)
  outliers start: 26
  outliers final: 17
  residues processed: 229
  average time/residue: 0.0927
  time to fit residues: 27.7963
Evaluate side-chains
  240 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  103 TYR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  242 CYS
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0470
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
R 176 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.177672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.157833 restraints weight = 12012.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.53
r_work: 0.3931 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7231  Z= 0.126
  Angle     :  0.549   7.236   9793  Z= 0.283
  Chirality :  0.041   0.145   1119
  Planarity :  0.003   0.050   1231
  Dihedral  :  4.471  52.665    977
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.49 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.16 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.29), residues: 889
  helix:  2.18 (0.27), residues: 397
  sheet:  0.55 (0.38), residues: 179
  loop : -0.78 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 314 
 TYR   0.010   0.001   TYR R  79 
 PHE   0.013   0.001   PHE R 108 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7230)
  covalent geometry    : angle       0.54882 ( 9791)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       1.37010 (    2)
  hydrogen bonds       : bond        0.03868 (  387)
  hydrogen bonds       : angle       4.45817 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 220
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4420 (mmm160) cc_final: 0.3825 (mmm160)
REVERT: A   35 LYS cc_start: 0.7147 (mttp) cc_final: 0.6734 (mmtp)
REVERT: A   53 MET cc_start: 0.6918 (mmt) cc_final: 0.6515 (mmt)
REVERT: A  186 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5706 (tm-30)
REVERT: A  197 LYS cc_start: 0.7246 (mttt) cc_final: 0.6640 (mttt)
REVERT: A  199 PHE cc_start: 0.7678 (m-80) cc_final: 0.7399 (m-10)
REVERT: A  214 CYS cc_start: 0.7754 (m) cc_final: 0.7520 (m)
REVERT: A  240 MET cc_start: 0.6657 (tpt) cc_final: 0.6110 (tpt)
REVERT: A  258 TRP cc_start: 0.8273 (m100) cc_final: 0.7702 (m100)
REVERT: A  271 LYS cc_start: 0.7679 (pttp) cc_final: 0.7400 (pttp)
REVERT: A  277 LYS cc_start: 0.6562 (mttm) cc_final: 0.6174 (mttm)
REVERT: A  302 TYR cc_start: 0.6193 (t80) cc_final: 0.5693 (t80)
REVERT: A  322 HIS cc_start: 0.7520 (t70) cc_final: 0.6821 (t70)
REVERT: A  342 VAL cc_start: 0.7463 (t) cc_final: 0.7141 (m)
REVERT: A  348 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6548 (tp)
REVERT: R   29 ILE cc_start: 0.7511 (mt) cc_final: 0.7284 (mt)
REVERT: R   95 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5700 (m-80)
REVERT: R  121 MET cc_start: 0.6751 (mmm) cc_final: 0.6463 (mmm)
REVERT: R  151 LEU cc_start: 0.6335 (tp) cc_final: 0.5784 (tp)
REVERT: R  154 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7073 (mm)
REVERT: R  235 CYS cc_start: 0.8434 (t) cc_final: 0.8109 (t)
REVERT: R  242 CYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7472 (t)
REVERT: R  268 ARG cc_start: 0.5323 (ttp-110) cc_final: 0.4850 (ttp-170)
REVERT: B   52 ARG cc_start: 0.7702 (ptp-110) cc_final: 0.7347 (ptp90)
REVERT: B   96 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7179 (mtt90)
REVERT: B  134 ARG cc_start: 0.6644 (ptp-110) cc_final: 0.6318 (mtm110)
REVERT: B  155 ASN cc_start: 0.7958 (m-40) cc_final: 0.7637 (m-40)
REVERT: B  175 GLN cc_start: 0.7421 (mm110) cc_final: 0.6877 (mm110)
REVERT: B  191 SER cc_start: 0.8399 (t) cc_final: 0.8139 (p)
REVERT: B  217 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6785 (tmm)
REVERT: B  220 GLN cc_start: 0.7565 (mt0) cc_final: 0.7167 (mt0)
REVERT: B  223 THR cc_start: 0.7284 (p) cc_final: 0.7060 (m)
REVERT: B  277 SER cc_start: 0.8086 (t) cc_final: 0.7443 (p)
REVERT: B  284 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6624 (mp)
REVERT: B  298 ASP cc_start: 0.8075 (t0) cc_final: 0.7820 (t0)
REVERT: B  325 MET cc_start: 0.6768 (tpp) cc_final: 0.6010 (tpp)
REVERT: C   21 MET cc_start: 0.7240 (mtm) cc_final: 0.6717 (mtm)
REVERT: C   44 HIS cc_start: 0.7007 (m90) cc_final: 0.6626 (m90)
REVERT: C   47 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6518 (mt-10)
  outliers start: 29
  outliers final: 18
  residues processed: 230
  average time/residue: 0.0905
  time to fit residues: 27.6194
Evaluate side-chains
  243 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  103 TYR
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  242 CYS
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0010
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 GLN
R 101 ASN
R 176 ASN
B 142 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.178889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.159037 restraints weight = 12104.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.53
r_work: 0.3931 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7231  Z= 0.130
  Angle     :  0.557   8.701   9793  Z= 0.287
  Chirality :  0.041   0.143   1119
  Planarity :  0.003   0.050   1231
  Dihedral  :  4.360  52.214    975
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.60 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 19.63 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.29), residues: 889
  helix:  2.32 (0.27), residues: 388
  sheet:  0.52 (0.38), residues: 179
  loop : -0.85 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.010   0.001   TYR B 124 
 PHE   0.014   0.001   PHE A 274 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7230)
  covalent geometry    : angle       0.55686 ( 9791)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       1.24264 (    2)
  hydrogen bonds       : bond        0.03899 (  387)
  hydrogen bonds       : angle       4.53052 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4449 (mmm160) cc_final: 0.3797 (mmm160)
REVERT: A   35 LYS cc_start: 0.7117 (mttp) cc_final: 0.6699 (mmtp)
REVERT: A   53 MET cc_start: 0.6912 (mmt) cc_final: 0.6521 (mmt)
REVERT: A  186 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5672 (tm-30)
REVERT: A  197 LYS cc_start: 0.7240 (mttt) cc_final: 0.6661 (mttt)
REVERT: A  199 PHE cc_start: 0.7628 (m-80) cc_final: 0.7345 (m-10)
REVERT: A  214 CYS cc_start: 0.7753 (m) cc_final: 0.7508 (m)
REVERT: A  240 MET cc_start: 0.6649 (tpt) cc_final: 0.6103 (tpt)
REVERT: A  250 PHE cc_start: 0.7629 (t80) cc_final: 0.7207 (t80)
REVERT: A  258 TRP cc_start: 0.8271 (m100) cc_final: 0.7686 (m100)
REVERT: A  271 LYS cc_start: 0.7677 (pttp) cc_final: 0.7405 (pttp)
REVERT: A  277 LYS cc_start: 0.6500 (mttm) cc_final: 0.6118 (mttm)
REVERT: A  302 TYR cc_start: 0.6191 (t80) cc_final: 0.5687 (t80)
REVERT: A  322 HIS cc_start: 0.7530 (t70) cc_final: 0.6819 (t70)
REVERT: A  342 VAL cc_start: 0.7471 (t) cc_final: 0.7146 (m)
REVERT: A  348 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6730 (tt)
REVERT: R   29 ILE cc_start: 0.7534 (mt) cc_final: 0.7308 (mt)
REVERT: R   95 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5683 (m-80)
REVERT: R  121 MET cc_start: 0.6752 (mmm) cc_final: 0.6444 (mmm)
REVERT: R  151 LEU cc_start: 0.6349 (tp) cc_final: 0.5782 (tp)
REVERT: R  154 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7080 (mm)
REVERT: R  242 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7523 (t)
REVERT: R  255 LEU cc_start: 0.7778 (mt) cc_final: 0.7103 (mt)
REVERT: R  268 ARG cc_start: 0.5375 (ttp-110) cc_final: 0.4872 (ttp-170)
REVERT: R  300 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7213 (mmm-85)
REVERT: B   96 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7227 (mtt90)
REVERT: B  134 ARG cc_start: 0.6636 (ptp-110) cc_final: 0.6315 (mtm110)
REVERT: B  155 ASN cc_start: 0.7945 (m-40) cc_final: 0.7638 (m-40)
REVERT: B  175 GLN cc_start: 0.7460 (mm110) cc_final: 0.6915 (mm110)
REVERT: B  191 SER cc_start: 0.8411 (t) cc_final: 0.8177 (p)
REVERT: B  217 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6758 (tmm)
REVERT: B  220 GLN cc_start: 0.7567 (mt0) cc_final: 0.7151 (mt0)
REVERT: B  277 SER cc_start: 0.8076 (t) cc_final: 0.7467 (p)
REVERT: B  284 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6600 (mp)
REVERT: B  298 ASP cc_start: 0.8095 (t0) cc_final: 0.7822 (t0)
REVERT: B  315 VAL cc_start: 0.7785 (p) cc_final: 0.7561 (m)
REVERT: B  325 MET cc_start: 0.6709 (tpp) cc_final: 0.6052 (tpp)
REVERT: C   21 MET cc_start: 0.7242 (mtm) cc_final: 0.6677 (mtm)
REVERT: C   44 HIS cc_start: 0.7037 (m90) cc_final: 0.6710 (m90)
REVERT: C   47 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6539 (mt-10)
  outliers start: 33
  outliers final: 21
  residues processed: 236
  average time/residue: 0.0950
  time to fit residues: 29.4257
Evaluate side-chains
  248 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 220
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   19 TYR
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  103 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  242 CYS
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
R 176 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.176525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.156466 restraints weight = 11932.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 3.46
r_work: 0.3896 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7231  Z= 0.214
  Angle     :  0.628   9.886   9793  Z= 0.329
  Chirality :  0.044   0.145   1119
  Planarity :  0.004   0.055   1231
  Dihedral  :  4.658  49.203    975
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 20.68 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.29), residues: 889
  helix:  2.09 (0.26), residues: 388
  sheet:  0.24 (0.37), residues: 183
  loop : -0.91 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 268 
 TYR   0.014   0.001   TYR B 124 
 PHE   0.018   0.002   PHE B 199 
 TRP   0.024   0.002   TRP B  82 
 HIS   0.011   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 7230)
  covalent geometry    : angle       0.62808 ( 9791)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       1.43603 (    2)
  hydrogen bonds       : bond        0.04520 (  387)
  hydrogen bonds       : angle       4.87414 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 226
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4548 (mmm160) cc_final: 0.4114 (mmm160)
REVERT: A   35 LYS cc_start: 0.7168 (mttp) cc_final: 0.6721 (mmtp)
REVERT: A   53 MET cc_start: 0.6886 (mmt) cc_final: 0.6467 (mmt)
REVERT: A  186 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5763 (tm-30)
REVERT: A  197 LYS cc_start: 0.7283 (mttt) cc_final: 0.6727 (mttt)
REVERT: A  198 MET cc_start: 0.7340 (ttt) cc_final: 0.7014 (ttm)
REVERT: A  199 PHE cc_start: 0.7636 (m-80) cc_final: 0.7366 (m-10)
REVERT: A  214 CYS cc_start: 0.7822 (m) cc_final: 0.7604 (m)
REVERT: A  224 CYS cc_start: 0.7728 (m) cc_final: 0.7071 (t)
REVERT: A  240 MET cc_start: 0.6675 (tpt) cc_final: 0.6163 (tpt)
REVERT: A  250 PHE cc_start: 0.7682 (t80) cc_final: 0.7263 (t80)
REVERT: A  258 TRP cc_start: 0.8289 (m100) cc_final: 0.7768 (m100)
REVERT: A  271 LYS cc_start: 0.7794 (pttp) cc_final: 0.7524 (pttp)
REVERT: A  277 LYS cc_start: 0.6477 (mttm) cc_final: 0.6084 (mttm)
REVERT: A  302 TYR cc_start: 0.6280 (t80) cc_final: 0.5694 (t80)
REVERT: A  322 HIS cc_start: 0.7546 (t70) cc_final: 0.6851 (t70)
REVERT: A  348 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6710 (tt)
REVERT: R   29 ILE cc_start: 0.7603 (mt) cc_final: 0.7399 (mt)
REVERT: R   95 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5649 (m-80)
REVERT: R  119 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7379 (m-80)
REVERT: R  121 MET cc_start: 0.6962 (mmm) cc_final: 0.6588 (mmm)
REVERT: R  151 LEU cc_start: 0.6445 (tp) cc_final: 0.5848 (tp)
REVERT: R  154 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7134 (mm)
REVERT: R  255 LEU cc_start: 0.7767 (mt) cc_final: 0.7410 (mt)
REVERT: R  268 ARG cc_start: 0.5476 (ttp-110) cc_final: 0.4914 (ttp-170)
REVERT: R  271 LEU cc_start: 0.7623 (mt) cc_final: 0.7379 (mt)
REVERT: R  300 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7344 (mmm-85)
REVERT: B   96 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7287 (mtt180)
REVERT: B  134 ARG cc_start: 0.6615 (ptp-110) cc_final: 0.6294 (mtm110)
REVERT: B  155 ASN cc_start: 0.7958 (m-40) cc_final: 0.7666 (m-40)
REVERT: B  175 GLN cc_start: 0.7551 (mm110) cc_final: 0.7034 (mm110)
REVERT: B  191 SER cc_start: 0.8434 (t) cc_final: 0.8175 (p)
REVERT: B  217 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6758 (tmm)
REVERT: B  220 GLN cc_start: 0.7677 (mt0) cc_final: 0.7314 (mt0)
REVERT: B  277 SER cc_start: 0.8072 (t) cc_final: 0.7443 (p)
REVERT: B  325 MET cc_start: 0.6733 (tpp) cc_final: 0.6096 (tpp)
REVERT: B  333 ASP cc_start: 0.7077 (p0) cc_final: 0.6743 (p0)
REVERT: C   21 MET cc_start: 0.7313 (mtm) cc_final: 0.6738 (mtm)
REVERT: C   44 HIS cc_start: 0.7053 (m90) cc_final: 0.6622 (m90)
REVERT: C   47 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6613 (mt-10)
  outliers start: 36
  outliers final: 25
  residues processed: 242
  average time/residue: 0.0899
  time to fit residues: 28.7196
Evaluate side-chains
  252 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 221
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   19 TYR
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   80 LEU
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  103 TYR
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0040
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 GLN
B 142 HIS
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.175613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.156051 restraints weight = 12095.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 3.44
r_work: 0.3934 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7231  Z= 0.125
  Angle     :  0.590   9.431   9793  Z= 0.300
  Chirality :  0.041   0.143   1119
  Planarity :  0.003   0.050   1231
  Dihedral  :  4.482  51.852    975
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.37 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.38 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.29), residues: 889
  helix:  2.22 (0.27), residues: 388
  sheet:  0.25 (0.38), residues: 183
  loop : -0.84 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.011   0.001   TYR R 292 
 PHE   0.012   0.001   PHE B 253 
 TRP   0.019   0.002   TRP B 297 
 HIS   0.013   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7230)
  covalent geometry    : angle       0.58972 ( 9791)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       1.17071 (    2)
  hydrogen bonds       : bond        0.03987 (  387)
  hydrogen bonds       : angle       4.63266 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4416 (mmm160) cc_final: 0.3755 (mmm160)
REVERT: A   35 LYS cc_start: 0.7095 (mttp) cc_final: 0.6680 (mmtp)
REVERT: A   53 MET cc_start: 0.6850 (mmt) cc_final: 0.6435 (mmt)
REVERT: A  186 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5723 (tm-30)
REVERT: A  197 LYS cc_start: 0.7249 (mttt) cc_final: 0.6749 (mttt)
REVERT: A  199 PHE cc_start: 0.7617 (m-80) cc_final: 0.7301 (m-10)
REVERT: A  214 CYS cc_start: 0.7805 (m) cc_final: 0.7562 (m)
REVERT: A  240 MET cc_start: 0.6636 (tpt) cc_final: 0.6115 (tpt)
REVERT: A  250 PHE cc_start: 0.7655 (t80) cc_final: 0.7233 (t80)
REVERT: A  258 TRP cc_start: 0.8280 (m100) cc_final: 0.7695 (m100)
REVERT: A  271 LYS cc_start: 0.7739 (pttp) cc_final: 0.7469 (pttp)
REVERT: A  277 LYS cc_start: 0.6465 (mttm) cc_final: 0.6078 (mttm)
REVERT: A  302 TYR cc_start: 0.6217 (t80) cc_final: 0.5714 (t80)
REVERT: A  322 HIS cc_start: 0.7515 (t70) cc_final: 0.6825 (t70)
REVERT: A  342 VAL cc_start: 0.7499 (t) cc_final: 0.7175 (m)
REVERT: A  348 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6916 (tt)
REVERT: R   29 ILE cc_start: 0.7478 (mt) cc_final: 0.7272 (mt)
REVERT: R   95 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5497 (m-80)
REVERT: R  121 MET cc_start: 0.6846 (mmm) cc_final: 0.6495 (mmm)
REVERT: R  146 CYS cc_start: 0.6946 (m) cc_final: 0.6606 (m)
REVERT: R  151 LEU cc_start: 0.6399 (tp) cc_final: 0.5826 (tp)
REVERT: R  154 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7122 (mm)
REVERT: R  268 ARG cc_start: 0.5358 (ttp-110) cc_final: 0.4863 (ttp-170)
REVERT: R  300 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7300 (mmm-85)
REVERT: B   96 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7235 (mtt90)
REVERT: B  134 ARG cc_start: 0.6595 (ptp-110) cc_final: 0.6287 (mtm110)
REVERT: B  155 ASN cc_start: 0.7950 (m-40) cc_final: 0.7655 (m-40)
REVERT: B  175 GLN cc_start: 0.7487 (mm110) cc_final: 0.6952 (mm110)
REVERT: B  191 SER cc_start: 0.8394 (t) cc_final: 0.8172 (p)
REVERT: B  217 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6757 (tmm)
REVERT: B  220 GLN cc_start: 0.7627 (mt0) cc_final: 0.7227 (mt0)
REVERT: B  277 SER cc_start: 0.8077 (t) cc_final: 0.7500 (p)
REVERT: B  315 VAL cc_start: 0.7779 (p) cc_final: 0.7566 (m)
REVERT: B  325 MET cc_start: 0.6658 (tpp) cc_final: 0.5989 (tpp)
REVERT: C   21 MET cc_start: 0.7274 (mtm) cc_final: 0.6699 (mtm)
REVERT: C   44 HIS cc_start: 0.7029 (m90) cc_final: 0.6562 (m90)
REVERT: C   47 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6596 (mt-10)
  outliers start: 28
  outliers final: 21
  residues processed: 224
  average time/residue: 0.1012
  time to fit residues: 29.5927
Evaluate side-chains
  238 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 212
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   19 TYR
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  215 LYS
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 87 optimal weight:    0.0040
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0000
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 GLN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.178126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.158379 restraints weight = 11848.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 3.43
r_work: 0.3931 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7231  Z= 0.136
  Angle     :  0.595   8.905   9793  Z= 0.303
  Chirality :  0.042   0.143   1119
  Planarity :  0.003   0.050   1231
  Dihedral  :  4.477  51.088    975
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.82 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.77 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.29), residues: 889
  helix:  2.22 (0.27), residues: 388
  sheet:  0.24 (0.38), residues: 183
  loop : -0.81 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.010   0.001   TYR R 292 
 PHE   0.028   0.001   PHE R 108 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7230)
  covalent geometry    : angle       0.59448 ( 9791)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       1.07919 (    2)
  hydrogen bonds       : bond        0.04045 (  387)
  hydrogen bonds       : angle       4.66187 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 213
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.4417 (mmm160) cc_final: 0.3752 (mmm160)
REVERT: A   35 LYS cc_start: 0.7069 (mttp) cc_final: 0.6648 (mmtp)
REVERT: A   53 MET cc_start: 0.6845 (mmt) cc_final: 0.6434 (mmt)
REVERT: A  186 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5701 (tm-30)
REVERT: A  197 LYS cc_start: 0.7266 (mttt) cc_final: 0.6750 (mttt)
REVERT: A  199 PHE cc_start: 0.7594 (m-80) cc_final: 0.7265 (m-10)
REVERT: A  214 CYS cc_start: 0.7753 (m) cc_final: 0.7546 (m)
REVERT: A  240 MET cc_start: 0.6662 (tpt) cc_final: 0.6144 (tpt)
REVERT: A  250 PHE cc_start: 0.7656 (t80) cc_final: 0.7224 (t80)
REVERT: A  258 TRP cc_start: 0.8290 (m100) cc_final: 0.7715 (m100)
REVERT: A  271 LYS cc_start: 0.7746 (pttp) cc_final: 0.7481 (pttp)
REVERT: A  277 LYS cc_start: 0.6448 (mttm) cc_final: 0.6059 (mttm)
REVERT: A  302 TYR cc_start: 0.6209 (t80) cc_final: 0.5707 (t80)
REVERT: A  322 HIS cc_start: 0.7517 (t70) cc_final: 0.6817 (t70)
REVERT: A  342 VAL cc_start: 0.7480 (t) cc_final: 0.7170 (m)
REVERT: A  348 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6886 (tp)
REVERT: R   29 ILE cc_start: 0.7499 (mt) cc_final: 0.7294 (mt)
REVERT: R   95 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5465 (m-80)
REVERT: R  121 MET cc_start: 0.6884 (mmm) cc_final: 0.6522 (mmm)
REVERT: R  146 CYS cc_start: 0.6978 (m) cc_final: 0.6650 (m)
REVERT: R  151 LEU cc_start: 0.6428 (tp) cc_final: 0.5841 (tp)
REVERT: R  154 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7108 (mm)
REVERT: R  268 ARG cc_start: 0.5379 (ttp-110) cc_final: 0.4886 (ttp-170)
REVERT: R  300 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7321 (mmm-85)
REVERT: B   85 TYR cc_start: 0.7291 (m-80) cc_final: 0.7007 (m-80)
REVERT: B   96 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7246 (mtt90)
REVERT: B  129 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7602 (ttt90)
REVERT: B  134 ARG cc_start: 0.6589 (ptp-110) cc_final: 0.6283 (mtm110)
REVERT: B  155 ASN cc_start: 0.7978 (m-40) cc_final: 0.7677 (m-40)
REVERT: B  175 GLN cc_start: 0.7488 (mm110) cc_final: 0.6941 (mm110)
REVERT: B  191 SER cc_start: 0.8383 (t) cc_final: 0.8135 (p)
REVERT: B  217 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6719 (tmm)
REVERT: B  220 GLN cc_start: 0.7628 (mt0) cc_final: 0.7247 (mt0)
REVERT: B  277 SER cc_start: 0.8076 (t) cc_final: 0.7490 (p)
REVERT: B  325 MET cc_start: 0.6664 (tpp) cc_final: 0.5947 (tpp)
REVERT: B  333 ASP cc_start: 0.7042 (p0) cc_final: 0.6751 (p0)
REVERT: C   21 MET cc_start: 0.7302 (mtm) cc_final: 0.6723 (mtm)
REVERT: C   44 HIS cc_start: 0.7045 (m90) cc_final: 0.6560 (m90)
REVERT: C   47 GLU cc_start: 0.7568 (mt-10) cc_final: 0.6551 (mt-10)
  outliers start: 28
  outliers final: 19
  residues processed: 224
  average time/residue: 0.0930
  time to fit residues: 27.2422
Evaluate side-chains
  236 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   19 TYR
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 81 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0050
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0170
   overall best weight:    0.4232

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 GLN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.177132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.157479 restraints weight = 11971.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 3.42
r_work: 0.3950 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6512
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7231  Z= 0.117
  Angle     :  0.590   8.992   9793  Z= 0.299
  Chirality :  0.042   0.168   1119
  Planarity :  0.003   0.049   1231
  Dihedral  :  4.398  51.330    975
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.49 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.17 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.29), residues: 889
  helix:  2.22 (0.27), residues: 390
  sheet:  0.29 (0.38), residues: 183
  loop : -0.74 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.009   0.001   TYR R 292 
 PHE   0.035   0.001   PHE R 108 
 TRP   0.017   0.001   TRP B 297 
 HIS   0.010   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7230)
  covalent geometry    : angle       0.58983 ( 9791)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.99305 (    2)
  hydrogen bonds       : bond        0.03861 (  387)
  hydrogen bonds       : angle       4.59534 ( 1101)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.7023 (mttp) cc_final: 0.6609 (mmtp)
REVERT: A   53 MET cc_start: 0.6834 (mmt) cc_final: 0.6425 (mmt)
REVERT: A  186 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5651 (tm-30)
REVERT: A  197 LYS cc_start: 0.7215 (mttt) cc_final: 0.6725 (mttt)
REVERT: A  199 PHE cc_start: 0.7561 (m-80) cc_final: 0.7250 (m-10)
REVERT: A  214 CYS cc_start: 0.7781 (m) cc_final: 0.7556 (m)
REVERT: A  240 MET cc_start: 0.6606 (tpt) cc_final: 0.6101 (tpt)
REVERT: A  250 PHE cc_start: 0.7634 (t80) cc_final: 0.7193 (t80)
REVERT: A  258 TRP cc_start: 0.8274 (m100) cc_final: 0.7736 (m100)
REVERT: A  271 LYS cc_start: 0.7707 (pttp) cc_final: 0.7449 (pttp)
REVERT: A  277 LYS cc_start: 0.6475 (mttm) cc_final: 0.6077 (mttm)
REVERT: A  302 TYR cc_start: 0.6171 (t80) cc_final: 0.5708 (t80)
REVERT: A  322 HIS cc_start: 0.7489 (t70) cc_final: 0.6785 (t70)
REVERT: A  342 VAL cc_start: 0.7492 (t) cc_final: 0.7162 (m)
REVERT: R   29 ILE cc_start: 0.7473 (mt) cc_final: 0.7255 (mt)
REVERT: R   95 PHE cc_start: 0.5719 (OUTLIER) cc_final: 0.5406 (m-80)
REVERT: R  108 PHE cc_start: 0.6893 (m-10) cc_final: 0.6442 (m-10)
REVERT: R  121 MET cc_start: 0.6947 (mmm) cc_final: 0.6572 (mmm)
REVERT: R  146 CYS cc_start: 0.6936 (m) cc_final: 0.6647 (m)
REVERT: R  151 LEU cc_start: 0.6436 (tp) cc_final: 0.5871 (tp)
REVERT: R  154 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7115 (mm)
REVERT: R  227 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6467 (mtmm)
REVERT: R  268 ARG cc_start: 0.5418 (ttp-110) cc_final: 0.4941 (ttp-170)
REVERT: R  300 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7322 (mmm-85)
REVERT: B   85 TYR cc_start: 0.7263 (m-80) cc_final: 0.6977 (m-80)
REVERT: B   90 VAL cc_start: 0.8658 (t) cc_final: 0.8309 (p)
REVERT: B   96 ARG cc_start: 0.7415 (mtt180) cc_final: 0.7136 (mtt90)
REVERT: B  134 ARG cc_start: 0.6601 (ptp-110) cc_final: 0.6280 (mtm110)
REVERT: B  155 ASN cc_start: 0.7929 (m-40) cc_final: 0.7583 (m-40)
REVERT: B  175 GLN cc_start: 0.7463 (mm110) cc_final: 0.6915 (mm110)
REVERT: B  191 SER cc_start: 0.8369 (t) cc_final: 0.8126 (p)
REVERT: B  217 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6713 (tmm)
REVERT: B  220 GLN cc_start: 0.7616 (mt0) cc_final: 0.7210 (mt0)
REVERT: B  277 SER cc_start: 0.8074 (t) cc_final: 0.7503 (p)
REVERT: B  325 MET cc_start: 0.6669 (tpp) cc_final: 0.5939 (tpp)
REVERT: B  333 ASP cc_start: 0.7049 (p0) cc_final: 0.6743 (p0)
REVERT: C   21 MET cc_start: 0.7311 (mtm) cc_final: 0.6727 (mtm)
REVERT: C   44 HIS cc_start: 0.6992 (m90) cc_final: 0.6519 (m90)
REVERT: C   47 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6540 (mt-10)
  outliers start: 25
  outliers final: 16
  residues processed: 222
  average time/residue: 0.0930
  time to fit residues: 26.9873
Evaluate side-chains
  235 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 214
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  257 LYS
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain R residue   19 TYR
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   75 ARG
Chi-restraints excluded: chain R residue   95 PHE
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  176 ASN
Chi-restraints excluded: chain R residue  227 LYS
Chi-restraints excluded: chain R residue  229 LEU
Chi-restraints excluded: chain R residue  283 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0060
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0980
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.179969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.160207 restraints weight = 11980.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 3.46
r_work: 0.3950 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6513
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7231  Z= 0.121
  Angle     :  0.596   8.614   9793  Z= 0.302
  Chirality :  0.042   0.166   1119
  Planarity :  0.003   0.050   1231
  Dihedral  :  4.346  50.573    975
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.94 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.43 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.29), residues: 889
  helix:  2.24 (0.27), residues: 391
  sheet:  0.25 (0.37), residues: 188
  loop : -0.60 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.008   0.001   TYR R 292 
 PHE   0.031   0.001   PHE R 108 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.009   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7230)
  covalent geometry    : angle       0.59562 ( 9791)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.90200 (    2)
  hydrogen bonds       : bond        0.03834 (  387)
  hydrogen bonds       : angle       4.54046 ( 1101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1842.21 seconds
wall clock time: 32 minutes 25.06 seconds (1945.06 seconds total)