Starting phenix.real_space_refine
on Fri Aug 22 20:42:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xtq_33452/08_2025/7xtq_33452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xtq_33452/08_2025/7xtq_33452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xtq_33452/08_2025/7xtq_33452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xtq_33452/08_2025/7xtq_33452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xtq_33452/08_2025/7xtq_33452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xtq_33452/08_2025/7xtq_33452.cif"
  }
  resolution = 3.2
  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=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      2      4.86       5
     C    5066      2.51       5
     N    1420      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8010
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1897
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 229, 1886
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "C"
        Number of residues, atoms: 229, 1886
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1910
    Chain: "B"
      Number of atoms: 2612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2612
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2063
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 251}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'H8I': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 380 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2CARG A 380 " occ=0.62
  Time building chain proxies: 2.09, per 1000 atoms: 0.26
  Number of scatterers: 8010
  At special positions: 0
  Unit cell: (77.064, 114.582, 122.694, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      46     16.00
     O    1476      8.00
     N    1420      7.00
     C    5066      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 155 " distance=2.03

  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: 0.58
  Conformation dependent library (CDL) restraints added in 369.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      40.5% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.409A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 4.269A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.732A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.631A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 21 through 42
      removed outlier: 3.980A  pdb=" N   ASP R  42 " --> pdb=" O   GLY R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 67
    Processing helix  chain 'R' and resid 68 through 75
      Proline residue:  R  72  - end of helix
      removed outlier: 4.452A  pdb=" N   TRP R  75 " --> pdb=" O   PRO R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 116
      Proline residue:  R  92  - end of helix
    Processing helix  chain 'R' and resid 123 through 141
      removed outlier: 3.754A  pdb=" N   ALA R 127 " --> pdb=" O   SER R 123 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY R 134 " --> pdb=" O   LEU R 130 " (cutoff:3.500A)
      Proline residue:  R 135  - end of helix
    Processing helix  chain 'R' and resid 156 through 161
    Processing helix  chain 'R' and resid 162 through 174
      removed outlier: 3.975A  pdb=" N   LEU R 174 " --> pdb=" O   VAL R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 207
      removed outlier: 3.732A  pdb=" N   LEU R 202 " --> pdb=" O   ASP R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 252
      removed outlier: 4.603A  pdb=" N   GLY R 238 " --> pdb=" O   GLY R 234 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
      removed outlier: 4.192A  pdb=" N   GLU R 252 " --> pdb=" O   VAL R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 282
      removed outlier: 3.701A  pdb=" N   LEU R 265 " --> pdb=" O   THR R 261 " (cutoff:3.500A)
      Proline residue:  R 277  - end of helix
    Processing helix  chain 'R' and resid 284 through 289
      removed outlier: 3.522A  pdb=" N   THR R 288 " --> pdb=" O   ASP R 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.695A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.633A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.096A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.216A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.013A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.510A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.672A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.328A  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: 3.515A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.056A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.040A  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: 3.657A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.621A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.520A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1156 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2581
        1.34 -     1.45: 1237
        1.45 -     1.57: 4298
        1.57 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 8181
  Sorted by residual:
  bond pdb=" C1  H8I R 401 "
       pdb=" N2  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.352  1.407 -0.055 2.00e-02 2.50e+03 7.51e+00
  bond pdb=" C3  H8I R 401 "
       pdb=" N1  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.309  1.355 -0.046 2.00e-02 2.50e+03 5.31e+00
  bond pdb=" C7  H8I R 401 "
       pdb=" O1  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.365  1.403 -0.038 2.00e-02 2.50e+03 3.70e+00
  bond pdb=" C7  H8I R 401 "
       pdb=" C8  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.424 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" C2  H8I R 401 "
       pdb=" C3  H8I R 401 "
    ideal  model  delta    sigma   weight residual
    1.396  1.424 -0.028 2.00e-02 2.50e+03 2.02e+00
  ... (remaining 8176 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 10977
        2.76 -     5.52: 106
        5.52 -     8.29: 20
        8.29 -    11.05: 3
       11.05 -    13.81: 1
  Bond angle restraints: 11107
  Sorted by residual:
  angle pdb=" C2  H8I R 401 "
        pdb=" C1  H8I R 401 "
        pdb=" N2  H8I R 401 "
      ideal   model   delta    sigma   weight residual
     117.71  131.52  -13.81 3.00e+00 1.11e-01 2.12e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.63    3.57 9.60e-01 1.09e+00 1.39e+01
  angle pdb=" N   GLN B   9 "
        pdb=" CA  GLN B   9 "
        pdb=" CB  GLN B   9 "
      ideal   model   delta    sigma   weight residual
     110.28  115.61   -5.33 1.55e+00 4.16e-01 1.18e+01
  angle pdb=" C3  H8I R 401 "
        pdb=" O1  H8I R 401 "
        pdb=" C7  H8I R 401 "
      ideal   model   delta    sigma   weight residual
     119.25  129.24   -9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" C   PRO A 321 "
        pdb=" N   GLU A 322 "
        pdb=" CA  GLU A 322 "
      ideal   model   delta    sigma   weight residual
     121.54  127.76   -6.22 1.91e+00 2.74e-01 1.06e+01
  ... (remaining 11102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 4501
       17.64 -    35.28: 326
       35.28 -    52.92: 51
       52.92 -    70.55: 9
       70.55 -    88.19: 4
  Dihedral angle restraints: 4891
    sinusoidal: 1920
      harmonic: 2971
  Sorted by residual:
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.97   42.03     1      1.00e+01 1.00e-02 2.47e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  PRO B 194 "
           pdb=" C   PRO B 194 "
           pdb=" N   ASP B 195 "
           pdb=" CA  ASP B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.07   15.93     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 4888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 796
       0.037 -    0.074: 307
       0.074 -    0.111: 112
       0.111 -    0.148: 22
       0.148 -    0.185: 5
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  GLN A  31 "
            pdb=" N   GLN A  31 "
            pdb=" C   GLN A  31 "
            pdb=" CB  GLN A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CB  THR B 223 "
            pdb=" CA  THR B 223 "
            pdb=" OG1 THR B 223 "
            pdb=" CG2 THR B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.59e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.46e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 134 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.85e+00
        pdb=" N   PRO R 135 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO R 135 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 135 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 228 "   -0.181 9.50e-02 1.11e+02   8.14e-02 4.28e+00
        pdb=" NE  ARG A 228 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 228 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 228 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 228 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO A 321 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 471
        2.73 -     3.27: 7767
        3.27 -     3.82: 13060
        3.82 -     4.36: 14743
        4.36 -     4.90: 26436
  Nonbonded interactions: 62477
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" OD1 ASN B 340 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.273 3.040
  ... (remaining 62472 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=0.38 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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.480
  Find NCS groups from input model:        0.020
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
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      :  0.004   0.055   8184  Z= 0.175
  Angle     :  0.745  13.809  11113  Z= 0.371
  Chirality :  0.046   0.185   1242
  Planarity :  0.005   0.081   1431
  Dihedral  : 12.535  88.193   2966
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 aren not related in a simple way.
  whole: -0.37 (0.26), residues: 1016
  helix:  1.49 (0.25), residues: 399
  sheet: -0.69 (0.34), residues: 215
  loop : -1.79 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 228 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.023   0.002   PHE A 212 
 TRP   0.015   0.001   TRP A 281 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8181)
  covalent geometry    : angle       0.74516 (11107)
  SS BOND              : bond        0.00492 (    3)
  SS BOND              : angle       0.81430 (    6)
  hydrogen bonds       : bond        0.16492 (  400)
  hydrogen bonds       : angle       6.32945 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6096 (mm-30)
REVERT: A  209 GLU cc_start: 0.6027 (tp30) cc_final: 0.5750 (tp30)
REVERT: A  210 THR cc_start: 0.8203 (p) cc_final: 0.7399 (m)
REVERT: A  228 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.7231 (ptt180)
REVERT: A  299 GLU cc_start: 0.7339 (tp30) cc_final: 0.6947 (tp30)
REVERT: A  392 GLU cc_start: 0.7115 (tp30) cc_final: 0.6546 (tp30)
REVERT: B   83 ASP cc_start: 0.7800 (t0) cc_final: 0.7335 (t70)
REVERT: B  148 CYS cc_start: 0.7185 (t) cc_final: 0.6952 (t)
REVERT: B  170 ASP cc_start: 0.6873 (t0) cc_final: 0.6569 (t0)
REVERT: B  197 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6439 (mtp180)
REVERT: B  214 ARG cc_start: 0.7301 (ptt90) cc_final: 0.6357 (ptt90)
REVERT: G   21 MET cc_start: 0.6969 (tmm) cc_final: 0.6692 (tmm)
REVERT: N   31 ASN cc_start: 0.8264 (m110) cc_final: 0.8024 (m110)
REVERT: N   43 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7855 (mmmt)
REVERT: R  248 VAL cc_start: 0.7218 (t) cc_final: 0.6969 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1027
  time to fit residues: 26.5799
Evaluate side-chains
  181 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0570
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0010
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0020
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.3112

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 119 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.138217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.116171 restraints weight = 22361.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.83
r_work: 0.3281 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8184  Z= 0.110
  Angle     :  0.603   9.532  11113  Z= 0.291
  Chirality :  0.042   0.173   1242
  Planarity :  0.004   0.052   1431
  Dihedral  :  4.963  64.603   1145
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.77 %
    Favored  : 90.17 %
  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 aren not related in a simple way.
  whole:  0.15 (0.26), residues: 1016
  helix:  2.06 (0.26), residues: 394
  sheet: -0.44 (0.34), residues: 205
  loop : -1.59 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 228 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8181)
  covalent geometry    : angle       0.60278 (11107)
  SS BOND              : bond        0.00219 (    3)
  SS BOND              : angle       0.48140 (    6)
  hydrogen bonds       : bond        0.03929 (  400)
  hydrogen bonds       : angle       4.56707 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 177
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   48 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8211 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7823 (mtt90)
REVERT: B  127 LYS cc_start: 0.7675 (mptt) cc_final: 0.7400 (mptt)
REVERT: B  197 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7280 (mtp180)
REVERT: B  214 ARG cc_start: 0.7911 (ptt90) cc_final: 0.7105 (ptt90)
REVERT: G   21 MET cc_start: 0.7464 (tmm) cc_final: 0.7080 (tmm)
REVERT: N   31 ASN cc_start: 0.8449 (m110) cc_final: 0.8024 (m-40)
REVERT: N   43 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7853 (mmmt)
REVERT: N   60 TYR cc_start: 0.8530 (m-80) cc_final: 0.8316 (m-80)
REVERT: R   80 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7458 (ttm-80)
REVERT: R  112 MET cc_start: 0.7900 (mmt) cc_final: 0.7619 (mpp)
  outliers start: 9
  outliers final: 4
  residues processed: 181
  average time/residue: 0.1099
  time to fit residues: 24.7210
Evaluate side-chains
  181 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 177
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   59 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 78 optimal weight:    0.2980
   chunk 93 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0040
   chunk 50 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.136810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.113918 restraints weight = 26138.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 4.19
r_work: 0.3172 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8184  Z= 0.112
  Angle     :  0.576   9.236  11113  Z= 0.277
  Chirality :  0.041   0.160   1242
  Planarity :  0.004   0.049   1431
  Dihedral  :  4.740  65.220   1145
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.80 %
    Favored  : 86.02 %
  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 aren not related in a simple way.
  whole:  0.42 (0.26), residues: 1016
  helix:  2.22 (0.26), residues: 400
  sheet: -0.23 (0.34), residues: 217
  loop : -1.48 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 187 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8181)
  covalent geometry    : angle       0.57567 (11107)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       0.48125 (    6)
  hydrogen bonds       : bond        0.03741 (  400)
  hydrogen bonds       : angle       4.24381 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B   48 ARG cc_start: 0.8546 (mmt180) cc_final: 0.8110 (mmt-90)
REVERT: B  126 LEU cc_start: 0.8138 (mm) cc_final: 0.7854 (mp)
REVERT: B  127 LYS cc_start: 0.7776 (mptt) cc_final: 0.7548 (mptt)
REVERT: B  197 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7478 (mtp180)
REVERT: B  214 ARG cc_start: 0.8004 (ptt90) cc_final: 0.7195 (ptt90)
REVERT: B  234 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8123 (m-80)
REVERT: B  241 PHE cc_start: 0.8600 (p90) cc_final: 0.8308 (p90)
REVERT: G   21 MET cc_start: 0.7602 (tmm) cc_final: 0.7188 (tmm)
REVERT: G   38 MET cc_start: 0.7535 (ttp) cc_final: 0.7311 (ttm)
REVERT: N   31 ASN cc_start: 0.8437 (m110) cc_final: 0.7991 (m-40)
REVERT: N   39 GLN cc_start: 0.8266 (tt0) cc_final: 0.8038 (tt0)
REVERT: N   43 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7850 (mmmt)
REVERT: N   60 TYR cc_start: 0.8580 (m-80) cc_final: 0.8307 (m-80)
REVERT: R  112 MET cc_start: 0.7954 (mmt) cc_final: 0.7636 (mpp)
  outliers start: 10
  outliers final: 4
  residues processed: 192
  average time/residue: 0.1067
  time to fit residues: 25.4371
Evaluate side-chains
  185 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 180
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
B 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.135640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117054 restraints weight = 11350.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.49
r_work: 0.3284 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8184  Z= 0.129
  Angle     :  0.573   9.640  11113  Z= 0.276
  Chirality :  0.042   0.161   1242
  Planarity :  0.004   0.048   1431
  Dihedral  :  4.734  65.991   1145
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.74 %
    Favored  : 84.72 %
  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 aren not related in a simple way.
  whole:  0.50 (0.26), residues: 1016
  helix:  2.23 (0.26), residues: 400
  sheet: -0.16 (0.34), residues: 216
  loop : -1.40 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 228 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8181)
  covalent geometry    : angle       0.57319 (11107)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.48448 (    6)
  hydrogen bonds       : bond        0.03833 (  400)
  hydrogen bonds       : angle       4.15596 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 200
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.5556 (OUTLIER) cc_final: 0.5341 (pm20)
REVERT: A   21 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6522 (mm-30)
REVERT: A  209 GLU cc_start: 0.7153 (tp30) cc_final: 0.6860 (tp30)
REVERT: A  210 THR cc_start: 0.8266 (m) cc_final: 0.7496 (m)
REVERT: A  228 ARG cc_start: 0.7814 (ptm-80) cc_final: 0.7541 (ptt180)
REVERT: A  392 GLU cc_start: 0.8009 (tp30) cc_final: 0.7696 (tp30)
REVERT: B   40 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7835 (p)
REVERT: B   48 ARG cc_start: 0.8589 (mmt180) cc_final: 0.8150 (mmt-90)
REVERT: B   61 MET cc_start: 0.7859 (ppp) cc_final: 0.7516 (ppp)
REVERT: B  126 LEU cc_start: 0.8243 (mm) cc_final: 0.7977 (mp)
REVERT: B  197 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7305 (mtp180)
REVERT: B  331 SER cc_start: 0.8560 (t) cc_final: 0.8352 (p)
REVERT: G   21 MET cc_start: 0.7661 (tmm) cc_final: 0.7230 (tmm)
REVERT: G   38 MET cc_start: 0.7640 (ttp) cc_final: 0.7416 (ttm)
REVERT: N   31 ASN cc_start: 0.8418 (m110) cc_final: 0.8021 (m-40)
REVERT: N   39 GLN cc_start: 0.8299 (tt0) cc_final: 0.8072 (tt0)
REVERT: N   43 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7835 (mmmt)
REVERT: N   60 TYR cc_start: 0.8608 (m-80) cc_final: 0.8343 (m-80)
REVERT: R  112 MET cc_start: 0.8076 (mmt) cc_final: 0.7759 (mpp)
  outliers start: 13
  outliers final: 6
  residues processed: 208
  average time/residue: 0.1177
  time to fit residues: 30.8262
Evaluate side-chains
  195 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 187
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 GLN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.135395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.114318 restraints weight = 17958.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.32
r_work: 0.3196 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8184  Z= 0.147
  Angle     :  0.598  10.206  11113  Z= 0.288
  Chirality :  0.042   0.141   1242
  Planarity :  0.004   0.051   1431
  Dihedral  :  4.771  65.381   1145
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.00 %
    Favored  : 82.46 %
  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 aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1016
  helix:  2.24 (0.26), residues: 400
  sheet: -0.14 (0.34), residues: 216
  loop : -1.37 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B  68 
 TYR   0.013   0.001   TYR N  60 
 PHE   0.016   0.001   PHE B 234 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8181)
  covalent geometry    : angle       0.59784 (11107)
  SS BOND              : bond        0.00391 (    3)
  SS BOND              : angle       0.54641 (    6)
  hydrogen bonds       : bond        0.03991 (  400)
  hydrogen bonds       : angle       4.18397 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 196
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6369 (mm-30)
REVERT: A  209 GLU cc_start: 0.6969 (tp30) cc_final: 0.6675 (tp30)
REVERT: A  210 THR cc_start: 0.8220 (m) cc_final: 0.7537 (m)
REVERT: A  228 ARG cc_start: 0.7869 (ptm-80) cc_final: 0.7509 (ptt180)
REVERT: A  230 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7067 (mm-30)
REVERT: A  392 GLU cc_start: 0.7814 (tp30) cc_final: 0.7486 (tp30)
REVERT: B   48 ARG cc_start: 0.8481 (mmt180) cc_final: 0.8260 (mmt-90)
REVERT: B  126 LEU cc_start: 0.7965 (mm) cc_final: 0.7636 (mt)
REVERT: B  197 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7111 (mtp180)
REVERT: G   21 MET cc_start: 0.7517 (tmm) cc_final: 0.7103 (tmm)
REVERT: G   38 MET cc_start: 0.7512 (ttp) cc_final: 0.7301 (ttm)
REVERT: N   31 ASN cc_start: 0.8349 (m110) cc_final: 0.7946 (m-40)
REVERT: N   43 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7762 (mmmt)
REVERT: N   60 TYR cc_start: 0.8580 (m-80) cc_final: 0.8319 (m-80)
REVERT: R  112 MET cc_start: 0.7912 (mmt) cc_final: 0.7549 (mpp)
  outliers start: 13
  outliers final: 9
  residues processed: 206
  average time/residue: 0.1359
  time to fit residues: 34.9209
Evaluate side-chains
  196 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 187
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.132906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.110367 restraints weight = 26550.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.93
r_work: 0.3152 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8184  Z= 0.145
  Angle     :  0.589  10.428  11113  Z= 0.283
  Chirality :  0.042   0.137   1242
  Planarity :  0.004   0.051   1431
  Dihedral  :  4.795  66.048   1145
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.59 %
    Favored  : 81.64 %
  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 aren not related in a simple way.
  whole:  0.60 (0.27), residues: 1016
  helix:  2.39 (0.26), residues: 393
  sheet: -0.12 (0.35), residues: 216
  loop : -1.35 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  68 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.013   0.001   PHE B 234 
 TRP   0.024   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8181)
  covalent geometry    : angle       0.58901 (11107)
  SS BOND              : bond        0.00390 (    3)
  SS BOND              : angle       0.53231 (    6)
  hydrogen bonds       : bond        0.04004 (  400)
  hydrogen bonds       : angle       4.12896 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6264 (mm-30)
REVERT: A   53 LYS cc_start: 0.7036 (ttpp) cc_final: 0.6819 (ttpp)
REVERT: A  209 GLU cc_start: 0.7016 (tp30) cc_final: 0.6706 (tp30)
REVERT: A  210 THR cc_start: 0.8103 (m) cc_final: 0.7483 (m)
REVERT: A  228 ARG cc_start: 0.7771 (ptm-80) cc_final: 0.7370 (ptt180)
REVERT: A  392 GLU cc_start: 0.7863 (tp30) cc_final: 0.7482 (tp30)
REVERT: B   40 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7819 (p)
REVERT: B   48 ARG cc_start: 0.8509 (mmt180) cc_final: 0.8270 (mmt-90)
REVERT: B   61 MET cc_start: 0.7733 (ppp) cc_final: 0.7428 (ppp)
REVERT: B  126 LEU cc_start: 0.7965 (mm) cc_final: 0.7687 (mt)
REVERT: B  197 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7226 (mtp180)
REVERT: B  219 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7663 (ttm-80)
REVERT: B  298 ASP cc_start: 0.8183 (t0) cc_final: 0.7960 (t0)
REVERT: G   21 MET cc_start: 0.7499 (tmm) cc_final: 0.7047 (tmm)
REVERT: G   38 MET cc_start: 0.7414 (ttp) cc_final: 0.7210 (ttm)
REVERT: N   31 ASN cc_start: 0.8298 (m110) cc_final: 0.8038 (m-40)
REVERT: N   43 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7699 (mmmt)
REVERT: N   60 TYR cc_start: 0.8547 (m-80) cc_final: 0.8168 (m-80)
REVERT: R  112 MET cc_start: 0.7715 (mmt) cc_final: 0.7325 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 199
  average time/residue: 0.1223
  time to fit residues: 30.4612
Evaluate side-chains
  201 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.128154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.106638 restraints weight = 24187.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 3.62
r_work: 0.3163 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8184  Z= 0.202
  Angle     :  0.640  12.660  11113  Z= 0.310
  Chirality :  0.044   0.149   1242
  Planarity :  0.005   0.056   1431
  Dihedral  :  5.014  67.063   1145
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.94 %
    Favored  : 80.69 %
  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 aren not related in a simple way.
  whole:  0.58 (0.27), residues: 1016
  helix:  2.30 (0.26), residues: 393
  sheet: -0.18 (0.34), residues: 233
  loop : -1.29 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 187 
 TYR   0.016   0.002   TYR N  60 
 PHE   0.016   0.002   PHE N 108 
 TRP   0.026   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8181)
  covalent geometry    : angle       0.63956 (11107)
  SS BOND              : bond        0.00526 (    3)
  SS BOND              : angle       0.73493 (    6)
  hydrogen bonds       : bond        0.04599 (  400)
  hydrogen bonds       : angle       4.24861 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6524 (mm-30)
REVERT: A  209 GLU cc_start: 0.7019 (tp30) cc_final: 0.6792 (tp30)
REVERT: A  210 THR cc_start: 0.8297 (m) cc_final: 0.7761 (m)
REVERT: A  228 ARG cc_start: 0.7967 (ptm-80) cc_final: 0.7711 (ptt180)
REVERT: A  392 GLU cc_start: 0.7896 (tp30) cc_final: 0.7569 (tp30)
REVERT: B   40 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7974 (p)
REVERT: B   43 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8172 (tp)
REVERT: B   48 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8285 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7876 (mtt90)
REVERT: B  126 LEU cc_start: 0.8117 (mm) cc_final: 0.7795 (mt)
REVERT: B  197 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7240 (mtp180)
REVERT: G   21 MET cc_start: 0.7517 (tmm) cc_final: 0.7111 (tmm)
REVERT: G   38 MET cc_start: 0.7624 (ttp) cc_final: 0.7398 (ttm)
REVERT: N   43 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7843 (mmmt)
REVERT: R  112 MET cc_start: 0.7999 (mmt) cc_final: 0.7641 (mpp)
  outliers start: 20
  outliers final: 13
  residues processed: 197
  average time/residue: 0.1155
  time to fit residues: 28.3726
Evaluate side-chains
  198 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 183
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0470
   chunk 64 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
G  44 HIS
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.130356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.109062 restraints weight = 22665.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.46
r_work: 0.3219 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8184  Z= 0.119
  Angle     :  0.581  10.083  11113  Z= 0.278
  Chirality :  0.041   0.138   1242
  Planarity :  0.004   0.052   1431
  Dihedral  :  4.790  67.093   1145
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.48 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.27), residues: 1016
  helix:  2.36 (0.26), residues: 400
  sheet: -0.05 (0.35), residues: 224
  loop : -1.22 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  68 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8181)
  covalent geometry    : angle       0.58085 (11107)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       0.47817 (    6)
  hydrogen bonds       : bond        0.03807 (  400)
  hydrogen bonds       : angle       4.08623 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6365 (mm-30)
REVERT: A  228 ARG cc_start: 0.7873 (ptm-80) cc_final: 0.7657 (ptt180)
REVERT: A  392 GLU cc_start: 0.7847 (tp30) cc_final: 0.7530 (tp30)
REVERT: B   40 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7938 (p)
REVERT: B   43 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (tp)
REVERT: B   48 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8305 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7822 (mtt90)
REVERT: B   61 MET cc_start: 0.7567 (ppp) cc_final: 0.7250 (ppp)
REVERT: B  126 LEU cc_start: 0.7946 (mm) cc_final: 0.7660 (mt)
REVERT: B  194 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8475 (Cg_endo)
REVERT: B  197 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7132 (mtp180)
REVERT: G   21 MET cc_start: 0.7455 (tmm) cc_final: 0.7066 (tmm)
REVERT: G   38 MET cc_start: 0.7572 (ttp) cc_final: 0.7362 (ttm)
REVERT: N   43 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7830 (mmmt)
REVERT: N   60 TYR cc_start: 0.8582 (m-80) cc_final: 0.8244 (m-80)
REVERT: R  112 MET cc_start: 0.7904 (mmt) cc_final: 0.7527 (mpp)
  outliers start: 14
  outliers final: 10
  residues processed: 195
  average time/residue: 0.1092
  time to fit residues: 26.5029
Evaluate side-chains
  197 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0570
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  53 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.108634 restraints weight = 23079.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 3.51
r_work: 0.3221 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8184  Z= 0.122
  Angle     :  0.594  10.190  11113  Z= 0.282
  Chirality :  0.041   0.135   1242
  Planarity :  0.004   0.053   1431
  Dihedral  :  4.717  67.040   1145
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.19 %
    Favored  : 79.03 %
  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 aren not related in a simple way.
  whole:  0.79 (0.27), residues: 1016
  helix:  2.40 (0.26), residues: 400
  sheet: -0.05 (0.34), residues: 228
  loop : -1.15 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  68 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE N 103 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8181)
  covalent geometry    : angle       0.59412 (11107)
  SS BOND              : bond        0.00353 (    3)
  SS BOND              : angle       0.47558 (    6)
  hydrogen bonds       : bond        0.03752 (  400)
  hydrogen bonds       : angle       4.05107 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6392 (mm-30)
REVERT: A  228 ARG cc_start: 0.7889 (ptm-80) cc_final: 0.7675 (ptt180)
REVERT: A  392 GLU cc_start: 0.7854 (tp30) cc_final: 0.7539 (tp30)
REVERT: B   40 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7969 (p)
REVERT: B   43 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (tp)
REVERT: B   48 ARG cc_start: 0.8512 (mmt180) cc_final: 0.8307 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7782 (mtt90)
REVERT: B   61 MET cc_start: 0.7543 (ppp) cc_final: 0.7243 (ppp)
REVERT: B  126 LEU cc_start: 0.7944 (mm) cc_final: 0.7689 (mt)
REVERT: B  194 PRO cc_start: 0.8681 (Cg_exo) cc_final: 0.8449 (Cg_endo)
REVERT: B  197 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7148 (mtp180)
REVERT: B  318 LEU cc_start: 0.8016 (tp) cc_final: 0.7811 (tt)
REVERT: G   21 MET cc_start: 0.7465 (tmm) cc_final: 0.7078 (tmm)
REVERT: G   38 MET cc_start: 0.7622 (ttp) cc_final: 0.7403 (ttm)
REVERT: N   43 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7814 (mmmt)
REVERT: N   60 TYR cc_start: 0.8593 (m-80) cc_final: 0.8319 (m-80)
REVERT: R  112 MET cc_start: 0.7915 (mmt) cc_final: 0.7540 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 198
  average time/residue: 0.1157
  time to fit residues: 28.7752
Evaluate side-chains
  200 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 188
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  170 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 71 optimal weight:    0.0060
   overall best weight:    0.3672

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.115457 restraints weight = 18355.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 3.31
r_work: 0.3252 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8184  Z= 0.104
  Angle     :  0.586  10.136  11113  Z= 0.276
  Chirality :  0.041   0.136   1242
  Planarity :  0.004   0.051   1431
  Dihedral  :  4.584  66.677   1145
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 19.91 %
    Favored  : 78.55 %
  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 aren not related in a simple way.
  whole:  0.88 (0.27), residues: 1016
  helix:  2.50 (0.26), residues: 400
  sheet:  0.01 (0.34), residues: 224
  loop : -1.14 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 187 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.009   0.001   PHE B 234 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8181)
  covalent geometry    : angle       0.58601 (11107)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       0.45433 (    6)
  hydrogen bonds       : bond        0.03432 (  400)
  hydrogen bonds       : angle       3.96443 ( 1156)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 182
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8136 (m-80) cc_final: 0.7929 (m-80)
REVERT: B   40 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7951 (p)
REVERT: B   48 ARG cc_start: 0.8513 (mmt180) cc_final: 0.8202 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7725 (mtt90)
REVERT: B   61 MET cc_start: 0.7418 (ppp) cc_final: 0.7159 (ppp)
REVERT: B  126 LEU cc_start: 0.7763 (mm) cc_final: 0.7513 (mt)
REVERT: B  197 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7117 (mtp180)
REVERT: B  296 VAL cc_start: 0.8224 (t) cc_final: 0.8013 (t)
REVERT: B  318 LEU cc_start: 0.8018 (tp) cc_final: 0.7804 (tt)
REVERT: G   21 MET cc_start: 0.7498 (tmm) cc_final: 0.7098 (tmm)
REVERT: G   38 MET cc_start: 0.7589 (ttp) cc_final: 0.7372 (ttm)
REVERT: N   43 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7833 (mmmt)
REVERT: N   60 TYR cc_start: 0.8574 (m-80) cc_final: 0.8359 (m-80)
REVERT: R  112 MET cc_start: 0.7933 (mmt) cc_final: 0.7563 (mpp)
  outliers start: 13
  outliers final: 12
  residues processed: 189
  average time/residue: 0.1225
  time to fit residues: 28.7515
Evaluate side-chains
  194 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 181
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  146 TRP
Chi-restraints excluded: chain R residue  280 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0020
   chunk 92 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.8790

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.111808 restraints weight = 17511.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.01
r_work: 0.3235 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8184  Z= 0.143
  Angle     :  0.619  10.743  11113  Z= 0.292
  Chirality :  0.042   0.139   1242
  Planarity :  0.004   0.052   1431
  Dihedral  :  4.666  66.564   1145
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 19.79 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.27), residues: 1016
  helix:  2.43 (0.26), residues: 400
  sheet:  0.00 (0.34), residues: 228
  loop : -1.14 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 187 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.024   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8181)
  covalent geometry    : angle       0.61933 (11107)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       0.47790 (    6)
  hydrogen bonds       : bond        0.03844 (  400)
  hydrogen bonds       : angle       3.98613 ( 1156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2160.22 seconds
wall clock time: 37 minutes 37.94 seconds (2257.94 seconds total)