Starting phenix.real_space_refine
on Sat Aug 23 23:56:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7a_38096/08_2025/8x7a_38096_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7a_38096/08_2025/8x7a_38096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x7a_38096/08_2025/8x7a_38096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7a_38096/08_2025/8x7a_38096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7a_38096/08_2025/8x7a_38096_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7a_38096/08_2025/8x7a_38096_neut_trim.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.029
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      56      5.16       5
     C    5028      2.51       5
     N    1399      2.21       5
     O    1466      1.98       5
     H    7679      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  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: 15628
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 3761
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 4782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 4782
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 7, 'TYR:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 87
    Chain: "G"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 851
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 1849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1849
          Classifications: {'peptide': 128}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 4357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 4357
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 14, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'Y9J': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.45, per 1000 atoms: 0.22
  Number of scatterers: 15628
  At special positions: 0
  Unit cell: (81.03, 106.58, 128.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     O    1466      8.00
     N    1399      7.00
     C    5028      6.00
     H    7679      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 439.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      42.0% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.678A  pdb=" N   ARG A 273 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.256A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 321 through 341
      removed outlier: 3.804A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 3.890A  pdb=" N   TYR A 381 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.502A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.704A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 19 through 41
      removed outlier: 3.608A  pdb=" N   GLY R  27 " --> pdb=" O   MET R  23 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 47 through 66
      removed outlier: 3.605A  pdb=" N   THR R  64 " --> pdb=" O   ASP R  60 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE R  66 " --> pdb=" O   LEU R  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 78
      removed outlier: 3.659A  pdb=" N   VAL R  71 " --> pdb=" O   LEU R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 123
      removed outlier: 4.768A  pdb=" N   CYS R  92 " --> pdb=" O   GLY R  88 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ALA R  94 " --> pdb=" O   ALA R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 129
    Processing helix  chain 'R' and resid 131 through 151
      Proline residue:  R 141  - end of helix
    Processing helix  chain 'R' and resid 152 through 157
    Processing helix  chain 'R' and resid 183 through 221
    Processing helix  chain 'R' and resid 233 through 264
      Proline residue:  R 254  - end of helix
    Processing helix  chain 'R' and resid 271 through 283
    Processing helix  chain 'R' and resid 283 through 292
      Proline residue:  R 289  - end of helix
    Processing helix  chain 'R' and resid 296 through 307
    Processing helix  chain 'R' and resid 307 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.562A  pdb=" N   PHE A 208 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 10.216A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.338A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.426A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.764A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.488A  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: 3.511A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.666A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 159 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.838A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.701A  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: 6.599A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.270A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.627A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL N  12 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 161 through 163

    411 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.93

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        0.82 -     1.25: 8967
        1.25 -     1.68: 6741
        1.68 -     2.11: 78
        2.11 -     2.54: 0
        2.54 -     2.97: 1
  Bond restraints: 15787
  Sorted by residual:
  bond pdb=" C   ALA B 203 "
       pdb=" N   ASP B 205 "
    ideal  model  delta    sigma   weight residual
    1.332  2.972 -1.639 1.40e-02 5.10e+03 1.37e+04
  bond pdb=" C15 Y9J R 401 "
       pdb=" C21 Y9J R 401 "
    ideal  model  delta    sigma   weight residual
    1.393  1.670 -0.277 2.00e-02 2.50e+03 1.92e+02
  bond pdb=" C19 Y9J R 401 "
       pdb=" C20 Y9J R 401 "
    ideal  model  delta    sigma   weight residual
    1.389  1.209  0.180 2.00e-02 2.50e+03 8.10e+01
  bond pdb=" C18 Y9J R 401 "
       pdb=" C19 Y9J R 401 "
    ideal  model  delta    sigma   weight residual
    1.394  1.215  0.179 2.00e-02 2.50e+03 8.05e+01
  bond pdb=" CA  MET R 244 "
       pdb=" C   MET R 244 "
    ideal  model  delta    sigma   weight residual
    1.524  1.422  0.102 1.26e-02 6.30e+03 6.50e+01
  ... (remaining 15782 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.53: 28349
       12.53 -    25.06: 6
       25.06 -    37.60: 1
       37.60 -    50.13: 0
       50.13 -    62.66: 2
  Bond angle restraints: 28358
  Sorted by residual:
  angle pdb=" O   ALA B 203 "
        pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     122.27   59.61   62.66 1.16e+00 7.43e-01 2.92e+03
  angle pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     118.79  150.01  -31.22 1.22e+00 6.72e-01 6.55e+02
  angle pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
        pdb=" H   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     124.38   66.43   57.95 3.00e+00 1.11e-01 3.73e+02
  angle pdb=" C14 Y9J R 401 "
        pdb=" C15 Y9J R 401 "
        pdb=" C21 Y9J R 401 "
      ideal   model   delta    sigma   weight residual
     121.72  143.69  -21.97 3.00e+00 1.11e-01 5.36e+01
  angle pdb=" C   ALA B 203 "
        pdb=" N   ASP B 205 "
        pdb=" CA  ASP B 205 "
      ideal   model   delta    sigma   weight residual
     121.54  135.26  -13.72 1.91e+00 2.74e-01 5.16e+01
  ... (remaining 28353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.03: 7234
       21.03 -    42.07: 193
       42.07 -    63.10: 73
       63.10 -    84.14: 10
       84.14 -   105.17: 1
  Dihedral angle restraints: 7511
    sinusoidal: 3974
      harmonic: 3537
  Sorted by residual:
  dihedral pdb=" CA  ALA B 203 "
           pdb=" C   ALA B 203 "
           pdb=" N   ASP B 205 "
           pdb=" CA  ASP B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -74.83 -105.17     0      5.00e+00 4.00e-02 4.42e+02
  dihedral pdb=" C   MET R 244 "
           pdb=" N   MET R 244 "
           pdb=" CA  MET R 244 "
           pdb=" CB  MET R 244 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.06  -12.54     0      2.50e+00 1.60e-01 2.51e+01
  dihedral pdb=" C   ALA R 265 "
           pdb=" N   ALA R 265 "
           pdb=" CA  ALA R 265 "
           pdb=" CB  ALA R 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.35   11.75     0      2.50e+00 1.60e-01 2.21e+01
  ... (remaining 7508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1158
       0.074 -    0.149: 86
       0.149 -    0.223: 5
       0.223 -    0.298: 1
       0.298 -    0.372: 1
  Chirality restraints: 1251
  Sorted by residual:
  chirality pdb=" CA  ALA R 265 "
            pdb=" N   ALA R 265 "
            pdb=" C   ALA R 265 "
            pdb=" CB  ALA R 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.11    0.37 2.00e-01 2.50e+01 3.46e+00
  chirality pdb=" CA  VAL R  25 "
            pdb=" N   VAL R  25 "
            pdb=" C   VAL R  25 "
            pdb=" CB  VAL R  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" C13 Y9J R 401 "
            pdb=" C12 Y9J R 401 "
            pdb=" C14 Y9J R 401 "
            pdb=" C9  Y9J R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1248 not shown)

  Planarity restraints: 2422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 203 "    0.036 2.00e-02 2.50e+03   2.16e-01 4.66e+02
        pdb=" N   ASP B 205 "   -0.362 2.00e-02 2.50e+03
        pdb=" CA  ASP B 205 "    0.141 2.00e-02 2.50e+03
        pdb=" H   ASP B 205 "    0.185 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 203 "    0.182 2.00e-02 2.50e+03   1.90e-01 3.60e+02
        pdb=" C   ALA B 203 "   -0.318 2.00e-02 2.50e+03
        pdb=" O   ALA B 203 "    0.062 2.00e-02 2.50e+03
        pdb=" N   ASP B 205 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  84 "    0.020 2.00e-02 2.50e+03   4.07e-02 1.66e+01
        pdb=" C   LEU R  84 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LEU R  84 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ALA R  85 "    0.024 2.00e-02 2.50e+03
  ... (remaining 2419 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 846
        2.21 -     2.80: 32540
        2.80 -     3.40: 42878
        3.40 -     4.00: 55049
        4.00 -     4.60: 86034
  Nonbonded interactions: 217347
  Sorted by model distance:
  nonbonded pdb=" O   SER B 189 "
            pdb=" HG  SER B 201 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" H   THR B 221 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" O   ASP B 170 "
            pdb=" H   GLY B 174 "
     model   vdw
     1.625 2.450
  nonbonded pdb="HD21 ASN R 203 "
            pdb=" OG1 THR R 245 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" O   LYS N  33 "
            pdb=" H   CYS N  99 "
     model   vdw
     1.645 2.450
  ... (remaining 217342 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.140
  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:             0.090
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     17.310
  Find NCS groups from input model:        0.060
  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:8.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
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      :  0.019   1.639   8108  Z= 1.342
  Angle     :  0.993  62.660  11001  Z= 0.688
  Chirality :  0.040   0.372   1251
  Planarity :  0.006   0.190   1419
  Dihedral  :  8.424 105.175   2894
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.22 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.21 %
  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: -0.63 (0.25), residues: 1028
  helix:  0.95 (0.25), residues: 394
  sheet: -0.65 (0.32), residues: 210
  loop : -1.59 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  41 
 TYR   0.023   0.001   TYR R  75 
 PHE   0.005   0.001   PHE R  24 
 TRP   0.004   0.001   TRP A 271 
 HIS   0.002   0.000   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.01910 ( 8108)
  covalent geometry    : angle       0.99318 (11001)
  hydrogen bonds       : bond        0.18165 (  411)
  hydrogen bonds       : angle       6.80820 ( 1164)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  314 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 313
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 313
  average time/residue: 1.0596
  time to fit residues: 351.3017
Evaluate side-chains
  181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
G  18 GLN
N   5 GLN
N  82 GLN
R 178 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.122406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.092536 restraints weight = 47762.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 3.43
r_work: 0.3373 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8108  Z= 0.208
  Angle     :  0.606   5.950  11001  Z= 0.322
  Chirality :  0.040   0.144   1251
  Planarity :  0.005   0.063   1419
  Dihedral  :  5.223  73.961   1171
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.52 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 19.80 %
    Favored  : 76.98 %
  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:  0.51 (0.26), residues: 1030
  helix:  2.07 (0.26), residues: 399
  sheet: -0.65 (0.31), residues: 248
  loop : -0.77 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 273 
 TYR   0.024   0.002   TYR A  37 
 PHE   0.011   0.001   PHE N  68 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.008   0.002   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8108)
  covalent geometry    : angle       0.60602 (11001)
  hydrogen bonds       : bond        0.03805 (  411)
  hydrogen bonds       : angle       4.75758 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  202 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 176
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.8617 (m-30) cc_final: 0.8403 (m-30)
REVERT: B  226 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7396 (tt0)
REVERT: N   46 GLU cc_start: 0.7373 (pt0) cc_final: 0.6925 (mm-30)
REVERT: R  107 MET cc_start: 0.8429 (tpp) cc_final: 0.8029 (tpt)
REVERT: R  138 LEU cc_start: 0.8580 (mm) cc_final: 0.8100 (tt)
  outliers start: 26
  outliers final: 13
  residues processed: 193
  average time/residue: 0.9135
  time to fit residues: 188.3819
Evaluate side-chains
  162 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  207 THR
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0270
   chunk 48 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.1840

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

Flipped N/Q/H residues before XYZ refinement:
N  39 GLN
R 178 GLN
R 284 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.120261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090595 restraints weight = 48323.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 3.53
r_work: 0.3324 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.5199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8108  Z= 0.132
  Angle     :  0.531   6.504  11001  Z= 0.274
  Chirality :  0.038   0.151   1251
  Planarity :  0.004   0.055   1419
  Dihedral  :  4.951  74.426   1171
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 21.91 %
    Favored  : 74.75 %
  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:  0.90 (0.26), residues: 1030
  helix:  2.44 (0.26), residues: 402
  sheet: -0.49 (0.31), residues: 247
  loop : -0.60 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 273 
 TYR   0.014   0.001   TYR A  37 
 PHE   0.017   0.001   PHE R 102 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8108)
  covalent geometry    : angle       0.53053 (11001)
  hydrogen bonds       : bond        0.03495 (  411)
  hydrogen bonds       : angle       4.33687 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.8593 (m-30) cc_final: 0.8366 (m-30)
REVERT: N   46 GLU cc_start: 0.7476 (pt0) cc_final: 0.7008 (mm-30)
REVERT: N   67 ARG cc_start: 0.6621 (ptp90) cc_final: 0.6315 (ptp90)
REVERT: N   82 GLN cc_start: 0.6831 (tp40) cc_final: 0.6334 (tp-100)
REVERT: R   41 ARG cc_start: 0.8035 (ptm-80) cc_final: 0.7306 (mpt-90)
REVERT: R   86 ARG cc_start: 0.5656 (OUTLIER) cc_final: 0.3781 (mtm180)
REVERT: R  107 MET cc_start: 0.8420 (tpp) cc_final: 0.8075 (tpt)
REVERT: R  138 LEU cc_start: 0.8596 (mm) cc_final: 0.8126 (tt)
  outliers start: 27
  outliers final: 13
  residues processed: 175
  average time/residue: 0.9487
  time to fit residues: 177.3818
Evaluate side-chains
  158 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  106 SER
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  234 GLU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  286 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 340 ASN
R 178 GLN
R 220 HIS
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.118441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.088476 restraints weight = 48095.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.51
r_work: 0.3288 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.5664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8108  Z= 0.151
  Angle     :  0.540   7.129  11001  Z= 0.278
  Chirality :  0.038   0.141   1251
  Planarity :  0.004   0.044   1419
  Dihedral  :  4.904  73.344   1171
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.92 %
    Favored  : 75.00 %
  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:  1.03 (0.27), residues: 1030
  helix:  2.66 (0.26), residues: 402
  sheet: -0.62 (0.31), residues: 252
  loop : -0.54 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  13 
 TYR   0.015   0.001   TYR A  37 
 PHE   0.015   0.001   PHE R 102 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8108)
  covalent geometry    : angle       0.53991 (11001)
  hydrogen bonds       : bond        0.03301 (  411)
  hydrogen bonds       : angle       4.19703 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 153
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8276 (mm-30)
REVERT: A   31 GLN cc_start: 0.8767 (mt0) cc_final: 0.8295 (tp40)
REVERT: A  368 ASP cc_start: 0.8688 (m-30) cc_final: 0.8467 (m-30)
REVERT: N   46 GLU cc_start: 0.7465 (pt0) cc_final: 0.7086 (mm-30)
REVERT: N   81 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7160 (tm)
REVERT: N   82 GLN cc_start: 0.6915 (tp40) cc_final: 0.6641 (tp-100)
REVERT: R   41 ARG cc_start: 0.8058 (ptm-80) cc_final: 0.7403 (mpt-90)
REVERT: R   86 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.3899 (mtm180)
REVERT: R   93 ASP cc_start: 0.8517 (m-30) cc_final: 0.8286 (m-30)
REVERT: R  138 LEU cc_start: 0.8649 (mm) cc_final: 0.8172 (tt)
  outliers start: 33
  outliers final: 9
  residues processed: 173
  average time/residue: 0.8218
  time to fit residues: 152.1468
Evaluate side-chains
  150 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  299 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
** R 237 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 = 0.3871 r_free = 0.3871 target = 0.116359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.086063 restraints weight = 48382.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 3.50
r_work: 0.3251 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.6135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8108  Z= 0.200
  Angle     :  0.575   7.277  11001  Z= 0.299
  Chirality :  0.040   0.235   1251
  Planarity :  0.004   0.044   1419
  Dihedral  :  5.073  73.492   1171
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.78 %
    Favored  : 74.63 %
  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:  1.06 (0.27), residues: 1030
  helix:  2.63 (0.26), residues: 403
  sheet: -0.64 (0.31), residues: 252
  loop : -0.42 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 273 
 TYR   0.016   0.002   TYR A  37 
 PHE   0.028   0.001   PHE R 102 
 TRP   0.012   0.002   TRP R 290 
 HIS   0.006   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8108)
  covalent geometry    : angle       0.57523 (11001)
  hydrogen bonds       : bond        0.03551 (  411)
  hydrogen bonds       : angle       4.28246 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8775 (mt0) cc_final: 0.8310 (tp40)
REVERT: A  368 ASP cc_start: 0.8771 (m-30) cc_final: 0.8383 (m-30)
REVERT: G   13 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8781 (tmm160)
REVERT: N   45 LEU cc_start: 0.5729 (pt) cc_final: 0.5492 (pt)
REVERT: N   46 GLU cc_start: 0.7535 (pt0) cc_final: 0.7233 (mm-30)
REVERT: N   82 GLN cc_start: 0.7034 (tp40) cc_final: 0.6596 (tp-100)
REVERT: R   41 ARG cc_start: 0.8109 (ptm-80) cc_final: 0.7483 (mpt180)
REVERT: R   86 ARG cc_start: 0.5647 (OUTLIER) cc_final: 0.3867 (mtm180)
REVERT: R   93 ASP cc_start: 0.8504 (m-30) cc_final: 0.8268 (m-30)
REVERT: R  107 MET cc_start: 0.8465 (tpp) cc_final: 0.8076 (tpt)
REVERT: R  138 LEU cc_start: 0.8576 (mm) cc_final: 0.8111 (tt)
REVERT: R  257 ILE cc_start: 0.9582 (mm) cc_final: 0.9333 (tp)
  outliers start: 29
  outliers final: 12
  residues processed: 165
  average time/residue: 0.8959
  time to fit residues: 158.6145
Evaluate side-chains
  150 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   64 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  286 ILE
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  299 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
R 163 GLN
** R 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.116747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.086265 restraints weight = 48090.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.54
r_work: 0.3264 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.6345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8108  Z= 0.140
  Angle     :  0.545   7.273  11001  Z= 0.279
  Chirality :  0.038   0.139   1251
  Planarity :  0.004   0.044   1419
  Dihedral  :  4.901  72.170   1171
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.14 %
    Favored  : 74.38 %
  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:  1.17 (0.27), residues: 1030
  helix:  2.80 (0.26), residues: 404
  sheet: -0.65 (0.31), residues: 253
  loop : -0.40 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 273 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.021   0.001   PHE R 102 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8108)
  covalent geometry    : angle       0.54475 (11001)
  hydrogen bonds       : bond        0.03293 (  411)
  hydrogen bonds       : angle       4.11248 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  164 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8773 (mt0) cc_final: 0.8313 (tp40)
REVERT: A  368 ASP cc_start: 0.8724 (m-30) cc_final: 0.8326 (m-30)
REVERT: B  264 TYR cc_start: 0.6615 (m-80) cc_final: 0.6114 (m-80)
REVERT: N   18 LEU cc_start: 0.7338 (tp) cc_final: 0.6862 (mp)
REVERT: N   45 LEU cc_start: 0.5804 (pt) cc_final: 0.5467 (pt)
REVERT: N   46 GLU cc_start: 0.7527 (pt0) cc_final: 0.7212 (mm-30)
REVERT: N   82 GLN cc_start: 0.6954 (tp40) cc_final: 0.6493 (tp-100)
REVERT: R   41 ARG cc_start: 0.8108 (ptm-80) cc_final: 0.7489 (mpt180)
REVERT: R   86 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.3904 (mtm180)
REVERT: R   93 ASP cc_start: 0.8519 (m-30) cc_final: 0.8278 (m-30)
REVERT: R  107 MET cc_start: 0.8462 (tpp) cc_final: 0.8042 (tpt)
REVERT: R  138 LEU cc_start: 0.8600 (mm) cc_final: 0.8146 (tt)
  outliers start: 20
  outliers final: 11
  residues processed: 161
  average time/residue: 0.9028
  time to fit residues: 155.2305
Evaluate side-chains
  150 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  234 GLU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  286 ILE
Chi-restraints excluded: chain R residue  299 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 89 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** R 237 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 = 0.3886 r_free = 0.3886 target = 0.116718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.086218 restraints weight = 47884.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 3.54
r_work: 0.3264 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.6447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8108  Z= 0.137
  Angle     :  0.540   7.412  11001  Z= 0.277
  Chirality :  0.038   0.138   1251
  Planarity :  0.004   0.044   1419
  Dihedral  :  4.839  71.438   1171
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 23.02 %
    Favored  : 74.26 %
  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:  1.30 (0.27), residues: 1030
  helix:  2.94 (0.26), residues: 403
  sheet: -0.62 (0.31), residues: 254
  loop : -0.33 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  13 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 102 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8108)
  covalent geometry    : angle       0.53967 (11001)
  hydrogen bonds       : bond        0.03199 (  411)
  hydrogen bonds       : angle       4.03954 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  162 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8777 (mt0) cc_final: 0.8318 (tp40)
REVERT: A  368 ASP cc_start: 0.8724 (m-30) cc_final: 0.8323 (m-30)
REVERT: G   13 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8781 (tmm160)
REVERT: N   45 LEU cc_start: 0.5743 (pt) cc_final: 0.5440 (pt)
REVERT: N   46 GLU cc_start: 0.7507 (pt0) cc_final: 0.7214 (mm-30)
REVERT: N   82 GLN cc_start: 0.6890 (tp40) cc_final: 0.6432 (tp-100)
REVERT: R   86 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.3843 (mtm180)
REVERT: R  107 MET cc_start: 0.8472 (tpp) cc_final: 0.8057 (tpt)
REVERT: R  138 LEU cc_start: 0.8587 (mm) cc_final: 0.8127 (tt)
  outliers start: 22
  outliers final: 13
  residues processed: 158
  average time/residue: 0.8755
  time to fit residues: 147.8992
Evaluate side-chains
  151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  220 HIS
Chi-restraints excluded: chain R residue  234 GLU
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  286 ILE
Chi-restraints excluded: chain R residue  287 LEU
Chi-restraints excluded: chain R residue  299 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** R 237 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 = 0.3911 r_free = 0.3911 target = 0.118340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.088646 restraints weight = 48268.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.49
r_work: 0.3326 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.6567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8108  Z= 0.112
  Angle     :  0.532   7.763  11001  Z= 0.271
  Chirality :  0.038   0.155   1251
  Planarity :  0.004   0.045   1419
  Dihedral  :  4.702  67.390   1171
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 23.89 %
    Favored  : 74.13 %
  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:  1.40 (0.27), residues: 1030
  helix:  3.03 (0.26), residues: 403
  sheet: -0.57 (0.32), residues: 253
  loop : -0.28 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  13 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.016   0.001   PHE R 102 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8108)
  covalent geometry    : angle       0.53224 (11001)
  hydrogen bonds       : bond        0.03086 (  411)
  hydrogen bonds       : angle       3.92800 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  155 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8799 (mt0) cc_final: 0.8341 (tp40)
REVERT: A  368 ASP cc_start: 0.8683 (m-30) cc_final: 0.8405 (m-30)
REVERT: G   13 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8713 (tmm160)
REVERT: N   45 LEU cc_start: 0.5758 (pt) cc_final: 0.5494 (pt)
REVERT: N   46 GLU cc_start: 0.7494 (pt0) cc_final: 0.7188 (mm-30)
REVERT: N   82 GLN cc_start: 0.6897 (tp40) cc_final: 0.6469 (tp-100)
REVERT: R   86 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.3702 (ttm170)
REVERT: R  107 MET cc_start: 0.8465 (tpp) cc_final: 0.8100 (tpt)
REVERT: R  138 LEU cc_start: 0.8596 (mm) cc_final: 0.8144 (tt)
  outliers start: 16
  outliers final: 8
  residues processed: 151
  average time/residue: 0.8608
  time to fit residues: 139.0535
Evaluate side-chains
  143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  220 HIS
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  299 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0070
   chunk 67 optimal weight:    0.6980
   chunk 80 optimal weight:   10.0000
   chunk 33 optimal weight:    0.3980
   chunk 99 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
** R 237 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 = 0.3905 r_free = 0.3905 target = 0.117961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.088111 restraints weight = 48455.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 3.54
r_work: 0.3348 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.6581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8108  Z= 0.103
  Angle     :  0.541   8.082  11001  Z= 0.274
  Chirality :  0.038   0.138   1251
  Planarity :  0.004   0.053   1419
  Dihedral  :  4.624  67.264   1171
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 25.25 %
    Favored  : 73.64 %
  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:  1.51 (0.27), residues: 1030
  helix:  3.14 (0.26), residues: 404
  sheet: -0.60 (0.32), residues: 251
  loop : -0.19 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 219 
 TYR   0.011   0.001   TYR A  37 
 PHE   0.015   0.001   PHE R 102 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8108)
  covalent geometry    : angle       0.54063 (11001)
  hydrogen bonds       : bond        0.02953 (  411)
  hydrogen bonds       : angle       3.78994 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8790 (mt0) cc_final: 0.8328 (tp40)
REVERT: A  368 ASP cc_start: 0.8631 (m-30) cc_final: 0.8401 (m-30)
REVERT: G   13 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8806 (tmm160)
REVERT: N   45 LEU cc_start: 0.5672 (pt) cc_final: 0.5424 (pt)
REVERT: N   46 GLU cc_start: 0.7371 (pt0) cc_final: 0.7071 (mm-30)
REVERT: N   82 GLN cc_start: 0.6872 (tp40) cc_final: 0.6427 (tp-100)
REVERT: R   86 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.3631 (ttm170)
REVERT: R  107 MET cc_start: 0.8436 (tpp) cc_final: 0.8078 (tpt)
REVERT: R  138 LEU cc_start: 0.8586 (mm) cc_final: 0.8126 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 151
  average time/residue: 0.9427
  time to fit residues: 152.0514
Evaluate side-chains
  142 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  252 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** R 237 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 = 0.3879 r_free = 0.3879 target = 0.116510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.086243 restraints weight = 48419.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 3.52
r_work: 0.3323 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.6782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8108  Z= 0.142
  Angle     :  0.566   8.254  11001  Z= 0.289
  Chirality :  0.038   0.137   1251
  Planarity :  0.004   0.042   1419
  Dihedral  :  4.708  65.886   1171
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 25.50 %
    Favored  : 73.64 %
  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:  1.49 (0.27), residues: 1030
  helix:  3.08 (0.26), residues: 404
  sheet: -0.52 (0.32), residues: 246
  loop : -0.23 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  13 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.019   0.001   PHE R 102 
 TRP   0.007   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8108)
  covalent geometry    : angle       0.56631 (11001)
  hydrogen bonds       : bond        0.03136 (  411)
  hydrogen bonds       : angle       3.89767 ( 1164)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   53 is missing expected H atoms. Skipping.
Residue LYS  216 is missing expected H atoms. Skipping.
Residue VAL  224 is missing expected H atoms. Skipping.
Residue VAL  248 is missing expected H atoms. Skipping.
Residue LEU  256 is missing expected H atoms. Skipping.
Residue LEU  260 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue TYR  105 is missing expected H atoms. Skipping.
Residue SER  108 is missing expected H atoms. Skipping.
Residue SER  147 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  320 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue VAL   30 is missing expected H atoms. Skipping.
Residue SER   25 is missing expected H atoms. Skipping.
Residue SER   30 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue THR  122 is missing expected H atoms. Skipping.
Residue SER   65 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Evaluate side-chains
  144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.8833 (mt0) cc_final: 0.8379 (tp40)
REVERT: A  368 ASP cc_start: 0.8732 (m-30) cc_final: 0.8330 (m-30)
REVERT: G   13 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8754 (tmm160)
REVERT: N   45 LEU cc_start: 0.5709 (pt) cc_final: 0.5498 (pt)
REVERT: N   46 GLU cc_start: 0.7426 (pt0) cc_final: 0.7159 (mm-30)
REVERT: R   86 ARG cc_start: 0.5599 (OUTLIER) cc_final: 0.3611 (ttm170)
REVERT: R  107 MET cc_start: 0.8450 (tpp) cc_final: 0.8048 (tpt)
REVERT: R  138 LEU cc_start: 0.8577 (mm) cc_final: 0.8117 (tt)
  outliers start: 7
  outliers final: 6
  residues processed: 143
  average time/residue: 0.9319
  time to fit residues: 142.4410
Evaluate side-chains
  139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  148 VAL
Chi-restraints excluded: chain R residue  252 SER
Chi-restraints excluded: chain R residue  255 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 237 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 = 0.3885 r_free = 0.3885 target = 0.116718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.086361 restraints weight = 48614.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.54
r_work: 0.3286 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.6836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8108  Z= 0.126
  Angle     :  0.557   8.308  11001  Z= 0.284
  Chirality :  0.038   0.138   1251
  Planarity :  0.004   0.043   1419
  Dihedral  :  4.695  65.672   1171
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 25.99 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.27), residues: 1030
  helix:  3.07 (0.26), residues: 404
  sheet: -0.49 (0.32), residues: 246
  loop : -0.21 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 219 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.021   0.001   PHE R 102 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8108)
  covalent geometry    : angle       0.55672 (11001)
  hydrogen bonds       : bond        0.03069 (  411)
  hydrogen bonds       : angle       3.86305 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5712.31 seconds
wall clock time: 97 minutes 12.23 seconds (5832.23 seconds total)