Starting phenix.real_space_refine
on Wed Sep 17 12:52:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y01_38800/09_2025/8y01_38800_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y01_38800/09_2025/8y01_38800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y01_38800/09_2025/8y01_38800_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y01_38800/09_2025/8y01_38800_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y01_38800/09_2025/8y01_38800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y01_38800/09_2025/8y01_38800.map"
  }
  resolution = 2.48
  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=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5575      2.51       5
     N    1475      2.21       5
     O    1589      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8705
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1570
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 2, 'TRANS': 202}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "B"
      Number of atoms: 2599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2599
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1751
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2327
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 18, 'TRANS': 279}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   TRP R 177 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CH2 TRP R 177 " occ=0.50
    residue:
      pdb=" N   PHE R 329 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE R 329 " occ=0.50
  Time building chain proxies: 2.16, per 1000 atoms: 0.25
  Number of scatterers: 8705
  At special positions: 0
  Unit cell: (89.64, 121.18, 126.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1589      8.00
     N    1475      7.00
     C    5575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 126 " - pdb=" SG  CYS R 203 " distance=1.59

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 396.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 15 sheets defined
      35.4% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.577A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.860A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.646A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.514A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.579A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.522A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'R' and resid 49 through 81
      removed outlier: 3.551A  pdb=" N   TYR R  53 " --> pdb=" O   PRO R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 117
      removed outlier: 4.074A  pdb=" N   SER R 107 " --> pdb=" O   THR R 103 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE R 109 " --> pdb=" O   ILE R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 122 through 157
    Processing helix  chain 'R' and resid 165 through 185
    Processing helix  chain 'R' and resid 214 through 228
      removed outlier: 4.445A  pdb=" N   SER R 218 " --> pdb=" O   PRO R 214 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE R 221 " --> pdb=" O   GLN R 217 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 253
    Processing helix  chain 'R' and resid 256 through 294
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 300 through 323
      removed outlier: 3.699A  pdb=" N   LEU R 306 " --> pdb=" O   LEU R 302 " (cutoff:3.500A)
      Proline residue:  R 307  - end of helix
      removed outlier: 3.784A  pdb=" N   ALA R 314 " --> pdb=" O   PHE R 310 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR R 315 " --> pdb=" O   ALA R 311 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE R 316 " --> pdb=" O   LYS R 312 " (cutoff:3.500A)
      Proline residue:  R 319  - end of helix
    Processing helix  chain 'R' and resid 326 through 335
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35
      removed outlier: 3.527A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.661A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.523A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.581A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.778A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.900A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.584A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.927A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.475A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.017A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP B 298 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.647A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.600A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.286A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.807A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160
      removed outlier: 3.505A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR S 213 " --> pdb=" O   SER S 206 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 194 through 196

    431 hydrogen bonds defined for protein.
    1230 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.07

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1548
        1.32 -     1.44: 2430
        1.44 -     1.57: 4839
        1.57 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 8911
  Sorted by residual:
  bond pdb=" C   LYS R 312 "
       pdb=" N   SER R 313 "
    ideal  model  delta    sigma   weight residual
    1.335  1.261  0.074 1.35e-02 5.49e+03 3.01e+01
  bond pdb=" N   LYS R 157 "
       pdb=" CA  LYS R 157 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.036 7.40e-03 1.83e+04 2.30e+01
  bond pdb=" C   GLY R 204 "
       pdb=" N   PRO R 205 "
    ideal  model  delta    sigma   weight residual
    1.332  1.391 -0.059 1.34e-02 5.57e+03 1.95e+01
  bond pdb=" N   PRO R 214 "
       pdb=" CD  PRO R 214 "
    ideal  model  delta    sigma   weight residual
    1.473  1.533 -0.060 1.40e-02 5.10e+03 1.84e+01
  bond pdb=" C   GLN R 114 "
       pdb=" N   VAL R 115 "
    ideal  model  delta    sigma   weight residual
    1.335  1.281  0.054 1.26e-02 6.30e+03 1.83e+01
  ... (remaining 8906 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.91: 12087
        6.91 -    13.82: 27
       13.82 -    20.73: 2
       20.73 -    27.64: 0
       27.64 -    34.55: 1
  Bond angle restraints: 12117
  Sorted by residual:
  angle pdb=" N   GLN S 231 "
        pdb=" CA  GLN S 231 "
        pdb=" C   GLN S 231 "
      ideal   model   delta    sigma   weight residual
     111.36  145.91  -34.55 1.09e+00 8.42e-01 1.00e+03
  angle pdb=" N   TYR R 194 "
        pdb=" CA  TYR R 194 "
        pdb=" C   TYR R 194 "
      ideal   model   delta    sigma   weight residual
     110.53   97.01   13.52 1.29e+00 6.01e-01 1.10e+02
  angle pdb=" N   ARG S 191 "
        pdb=" CA  ARG S 191 "
        pdb=" C   ARG S 191 "
      ideal   model   delta    sigma   weight residual
     108.38   98.07   10.31 1.35e+00 5.49e-01 5.83e+01
  angle pdb=" N   VAL R 320 "
        pdb=" CA  VAL R 320 "
        pdb=" C   VAL R 320 "
      ideal   model   delta    sigma   weight residual
     110.42  117.64   -7.22 9.60e-01 1.09e+00 5.65e+01
  angle pdb=" C   GLN S 231 "
        pdb=" CA  GLN S 231 "
        pdb=" CB  GLN S 231 "
      ideal   model   delta    sigma   weight residual
     110.85   98.66   12.19 1.70e+00 3.46e-01 5.14e+01
  ... (remaining 12112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.88: 4629
       11.88 -    23.75: 397
       23.75 -    35.63: 121
       35.63 -    47.50: 47
       47.50 -    59.38: 17
  Dihedral angle restraints: 5211
    sinusoidal: 1928
      harmonic: 3283
  Sorted by residual:
  dihedral pdb=" N   HIS S 232 "
           pdb=" C   HIS S 232 "
           pdb=" CA  HIS S 232 "
           pdb=" CB  HIS S 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  156.47  -33.67     0      2.50e+00 1.60e-01 1.81e+02
  dihedral pdb=" C   HIS S 232 "
           pdb=" N   HIS S 232 "
           pdb=" CA  HIS S 232 "
           pdb=" CB  HIS S 232 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.77   31.17     0      2.50e+00 1.60e-01 1.55e+02
  dihedral pdb=" N   GLN S 231 "
           pdb=" C   GLN S 231 "
           pdb=" CA  GLN S 231 "
           pdb=" CB  GLN S 231 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  149.40  -26.60     0      2.50e+00 1.60e-01 1.13e+02
  ... (remaining 5208 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.311: 1366
       0.311 -    0.623: 3
       0.623 -    0.934: 0
       0.934 -    1.246: 1
       1.246 -    1.557: 2
  Chirality restraints: 1372
  Sorted by residual:
  chirality pdb=" CA  GLN S 231 "
            pdb=" N   GLN S 231 "
            pdb=" C   GLN S 231 "
            pdb=" CB  GLN S 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.95    1.56 2.00e-01 2.50e+01 6.06e+01
  chirality pdb=" CA  HIS S 232 "
            pdb=" N   HIS S 232 "
            pdb=" C   HIS S 232 "
            pdb=" CB  HIS S 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.05    1.46 2.00e-01 2.50e+01 5.31e+01
  chirality pdb=" CA  TYR S 235 "
            pdb=" N   TYR S 235 "
            pdb=" C   TYR S 235 "
            pdb=" CB  TYR S 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.21e+01
  ... (remaining 1369 not shown)

  Planarity restraints: 1529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 RET R 401 "    0.181 2.00e-02 2.50e+03   1.18e-01 1.74e+02
        pdb=" C11 RET R 401 "   -0.143 2.00e-02 2.50e+03
        pdb=" C19 RET R 401 "    0.013 2.00e-02 2.50e+03
        pdb=" C8  RET R 401 "   -0.112 2.00e-02 2.50e+03
        pdb=" C9  RET R 401 "    0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 RET R 401 "   -0.075 2.00e-02 2.50e+03   7.18e-02 6.45e+01
        pdb=" C13 RET R 401 "    0.055 2.00e-02 2.50e+03
        pdb=" C14 RET R 401 "    0.098 2.00e-02 2.50e+03
        pdb=" C15 RET R 401 "   -0.087 2.00e-02 2.50e+03
        pdb=" C20 RET R 401 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C6  RET R 401 "   -0.055 2.00e-02 2.50e+03   5.32e-02 2.83e+01
        pdb=" C7  RET R 401 "    0.062 2.00e-02 2.50e+03
        pdb=" C8  RET R 401 "    0.043 2.00e-02 2.50e+03
        pdb=" C9  RET R 401 "   -0.051 2.00e-02 2.50e+03
  ... (remaining 1526 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 65
        2.58 -     3.16: 7208
        3.16 -     3.74: 13465
        3.74 -     4.32: 19463
        4.32 -     4.90: 32200
  Nonbonded interactions: 72401
  Sorted by model distance:
  nonbonded pdb=" O   TYR S 173 "
            pdb=" O   GLN S 231 "
     model   vdw
     1.998 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OD2 ASP A   9 "
            pdb=" ND2 ASN S 169 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.282 3.040
  ... (remaining 72396 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     8.370
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
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      :  0.013   0.443   8913  Z= 0.740
  Angle     :  1.362  34.552  12119  Z= 0.922
  Chirality :  0.102   1.557   1372
  Planarity :  0.007   0.118   1529
  Dihedral  : 11.411  59.378   3092
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.30 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  4.81 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.66 %
  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: -1.61 (0.24), residues: 1117
  helix:  0.85 (0.26), residues: 372
  sheet: -2.15 (0.29), residues: 270
  loop : -1.91 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  24 
 TYR   0.041   0.004   TYR S  94 
 PHE   0.035   0.004   PHE S 177 
 TRP   0.044   0.003   TRP S 111 
 HIS   0.022   0.003   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.01205 ( 8911)
  covalent geometry    : angle       1.36091 (12117)
  SS BOND              : bond        0.44298 (    1)
  SS BOND              : angle       4.57100 (    2)
  hydrogen bonds       : bond        0.19514 (  426)
  hydrogen bonds       : angle       7.11447 ( 1230)
  Misc. bond           : bond        0.12553 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 223
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8730 (ttmm)
REVERT: B   16 ASN cc_start: 0.8785 (m-40) cc_final: 0.7502 (m-40)
REVERT: B   19 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8580 (tmm-80)
REVERT: B   20 ASP cc_start: 0.9427 (m-30) cc_final: 0.8387 (m-30)
REVERT: G   31 SER cc_start: 0.8347 (t) cc_final: 0.7994 (m)
REVERT: G   42 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7958 (pp20)
REVERT: S   82 GLN cc_start: 0.8522 (tp40) cc_final: 0.8192 (tp-100)
REVERT: S  186 GLN cc_start: 0.8402 (mt0) cc_final: 0.8107 (tt0)
REVERT: S  217 SER cc_start: 0.8889 (m) cc_final: 0.8638 (p)
REVERT: S  219 LEU cc_start: 0.9505 (mp) cc_final: 0.9260 (mm)
REVERT: S  232 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.7885 (t-90)
REVERT: S  235 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: R   85 ARG cc_start: 0.8699 (mtm110) cc_final: 0.7782 (mtt-85)
REVERT: R  150 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7945 (mt-10)
REVERT: R  200 LYS cc_start: 0.8388 (mttt) cc_final: 0.8138 (mmtm)
REVERT: R  213 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5122 (m-80)
REVERT: R  263 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7959 (tm-30)
REVERT: R  273 MET cc_start: 0.8182 (mtp) cc_final: 0.7868 (mtt)
REVERT: R  326 ASN cc_start: 0.8755 (t0) cc_final: 0.8004 (t0)
REVERT: R  328 GLN cc_start: 0.8472 (mt0) cc_final: 0.8152 (mp10)
  outliers start: 24
  outliers final: 5
  residues processed: 241
  average time/residue: 0.6191
  time to fit residues: 157.6149
Evaluate side-chains
  172 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  232 HIS
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   59 TRP
Chi-restraints excluded: chain R residue  114 GLN
Chi-restraints excluded: chain R residue  213 TYR
Chi-restraints excluded: chain R residue  263 GLU
Chi-restraints excluded: chain R residue  284 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 346 ASN
B  91 HIS
B 220 GLN
B 259 GLN
G   5 ASN
S 142 GLN
R 331 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.106762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.073444 restraints weight = 14749.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.99
r_work: 0.2826 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8913  Z= 0.164
  Angle     :  0.637   8.935  12119  Z= 0.332
  Chirality :  0.045   0.258   1372
  Planarity :  0.005   0.056   1529
  Dihedral  :  6.447  57.445   1245
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 12.58 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.25), residues: 1117
  helix:  1.83 (0.26), residues: 383
  sheet: -1.68 (0.28), residues: 278
  loop : -1.50 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 197 
 TYR   0.021   0.002   TYR S 235 
 PHE   0.015   0.002   PHE R 208 
 TRP   0.016   0.001   TRP S 111 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8911)
  covalent geometry    : angle       0.63683 (12117)
  SS BOND              : bond        0.00515 (    1)
  SS BOND              : angle       0.46958 (    2)
  hydrogen bonds       : bond        0.05021 (  426)
  hydrogen bonds       : angle       5.10423 ( 1230)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 176
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8800 (mtp) cc_final: 0.8410 (mtt)
REVERT: A  298 GLU cc_start: 0.8877 (tt0) cc_final: 0.8633 (tt0)
REVERT: A  306 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8662 (mm110)
REVERT: A  354 PHE cc_start: 0.4980 (OUTLIER) cc_final: 0.4321 (m-10)
REVERT: B   16 ASN cc_start: 0.8718 (m-40) cc_final: 0.8229 (m-40)
REVERT: B   19 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8710 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8310 (mpt90) cc_final: 0.7937 (mpp80)
REVERT: B  215 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7535 (pt0)
REVERT: G   31 SER cc_start: 0.8070 (t) cc_final: 0.7680 (m)
REVERT: G   42 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8096 (pp20)
REVERT: S   82 GLN cc_start: 0.8279 (tp40) cc_final: 0.7877 (tp-100)
REVERT: S  186 GLN cc_start: 0.8527 (mt0) cc_final: 0.8147 (tt0)
REVERT: S  235 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6752 (t80)
REVERT: S  244 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8516 (ttpp)
REVERT: R   85 ARG cc_start: 0.8523 (mtm110) cc_final: 0.7672 (mtm-85)
REVERT: R  113 ASN cc_start: 0.8931 (m-40) cc_final: 0.8490 (t0)
REVERT: R  157 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8288 (mtpt)
REVERT: R  258 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7246 (t)
REVERT: R  263 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7285 (tm-30)
REVERT: R  265 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7363 (tt0)
  outliers start: 46
  outliers final: 11
  residues processed: 202
  average time/residue: 0.6554
  time to fit residues: 139.7641
Evaluate side-chains
  172 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  244 LYS
Chi-restraints excluded: chain R residue   59 TRP
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  258 SER
Chi-restraints excluded: chain R residue  263 GLU
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  313 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 239 ASN
B 259 GLN
S  39 GLN
R  89 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.105026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.071826 restraints weight = 14646.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.95
r_work: 0.2803 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8913  Z= 0.179
  Angle     :  0.599   9.256  12119  Z= 0.309
  Chirality :  0.043   0.263   1372
  Planarity :  0.005   0.056   1529
  Dihedral  :  5.899  59.739   1237
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 16.63 %
    Favored  : 78.99 %
  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: -0.17 (0.25), residues: 1117
  helix:  2.22 (0.26), residues: 385
  sheet: -1.45 (0.29), residues: 276
  loop : -1.26 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 197 
 TYR   0.023   0.002   TYR S 235 
 PHE   0.014   0.002   PHE B 199 
 TRP   0.015   0.001   TRP S 111 
 HIS   0.003   0.001   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8911)
  covalent geometry    : angle       0.59914 (12117)
  SS BOND              : bond        0.00305 (    1)
  SS BOND              : angle       0.12116 (    2)
  hydrogen bonds       : bond        0.04437 (  426)
  hydrogen bonds       : angle       4.79226 ( 1230)
  Misc. bond           : bond        0.00032 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 167
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8784 (mtp) cc_final: 0.8404 (mtm)
REVERT: A  306 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8616 (mm110)
REVERT: B   16 ASN cc_start: 0.8656 (m-40) cc_final: 0.8384 (m-40)
REVERT: B   19 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8724 (tmm-80)
REVERT: B   23 LYS cc_start: 0.9233 (tppp) cc_final: 0.9031 (tppp)
REVERT: B   46 ARG cc_start: 0.8255 (mpt90) cc_final: 0.7900 (mpp80)
REVERT: B  197 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7932 (mtp85)
REVERT: G   31 SER cc_start: 0.7997 (t) cc_final: 0.7766 (m)
REVERT: G   42 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8153 (pp20)
REVERT: S   82 GLN cc_start: 0.8264 (tp40) cc_final: 0.7827 (tp-100)
REVERT: S   87 ARG cc_start: 0.8808 (ptp-170) cc_final: 0.8583 (pmm-80)
REVERT: S  186 GLN cc_start: 0.8558 (mt0) cc_final: 0.8207 (tt0)
REVERT: S  235 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6810 (t80)
REVERT: S  244 LYS cc_start: 0.8847 (tttp) cc_final: 0.8551 (ttpp)
REVERT: R   85 ARG cc_start: 0.8539 (mtm110) cc_final: 0.7835 (mtm-85)
REVERT: R  113 ASN cc_start: 0.8912 (m-40) cc_final: 0.8402 (t0)
REVERT: R  125 MET cc_start: 0.7913 (tpp) cc_final: 0.7706 (tpp)
REVERT: R  157 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8290 (mtpt)
REVERT: R  200 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7999 (mmtp)
REVERT: R  258 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.7196 (t)
REVERT: R  263 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7370 (tm-30)
  outliers start: 40
  outliers final: 17
  residues processed: 187
  average time/residue: 0.6936
  time to fit residues: 136.7821
Evaluate side-chains
  179 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue  107 SER
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  258 SER
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 101 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 239 ASN
B 259 GLN
B 266 HIS
R 335 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.106876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.073953 restraints weight = 14712.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.97
r_work: 0.2841 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8913  Z= 0.123
  Angle     :  0.561   8.542  12119  Z= 0.286
  Chirality :  0.042   0.226   1372
  Planarity :  0.004   0.051   1529
  Dihedral  :  5.419  59.595   1232
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 17.72 %
    Favored  : 78.45 %
  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:  0.06 (0.26), residues: 1117
  helix:  2.38 (0.26), residues: 385
  sheet: -1.30 (0.28), residues: 277
  loop : -1.11 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  21 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.010   0.001   PHE B 151 
 TRP   0.025   0.001   TRP R  59 
 HIS   0.002   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8911)
  covalent geometry    : angle       0.56056 (12117)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       0.12358 (    2)
  hydrogen bonds       : bond        0.03964 (  426)
  hydrogen bonds       : angle       4.63669 ( 1230)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 173
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8861 (mtp) cc_final: 0.8457 (mtm)
REVERT: A  298 GLU cc_start: 0.8836 (tt0) cc_final: 0.8595 (tt0)
REVERT: A  306 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8563 (mm110)
REVERT: A  354 PHE cc_start: 0.5341 (OUTLIER) cc_final: 0.4225 (m-80)
REVERT: B   16 ASN cc_start: 0.8708 (m-40) cc_final: 0.7973 (m-40)
REVERT: B   19 ARG cc_start: 0.9034 (ttp80) cc_final: 0.8705 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8210 (mpt90) cc_final: 0.7842 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7983 (mtp85)
REVERT: B  215 GLU cc_start: 0.7887 (pt0) cc_final: 0.7422 (pt0)
REVERT: B  219 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8485 (ttm-80)
REVERT: G   31 SER cc_start: 0.8019 (t) cc_final: 0.7777 (m)
REVERT: G   42 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8156 (pp20)
REVERT: S   43 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8365 (mtmm)
REVERT: S   82 GLN cc_start: 0.8289 (tp40) cc_final: 0.7832 (tp-100)
REVERT: S   87 ARG cc_start: 0.8804 (ptp-170) cc_final: 0.8595 (pmm-80)
REVERT: S  186 GLN cc_start: 0.8512 (mt0) cc_final: 0.8139 (tt0)
REVERT: S  244 LYS cc_start: 0.8848 (tttp) cc_final: 0.8558 (ttpp)
REVERT: R   85 ARG cc_start: 0.8457 (mtm110) cc_final: 0.7604 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8805 (m-40) cc_final: 0.8309 (t0)
REVERT: R  157 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8286 (mtpt)
REVERT: R  200 LYS cc_start: 0.8276 (mmtp) cc_final: 0.8056 (mmtp)
REVERT: R  263 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7334 (tm-30)
REVERT: R  265 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7313 (tt0)
REVERT: R  303 MET cc_start: 0.7512 (tpp) cc_final: 0.7182 (ttp)
  outliers start: 35
  outliers final: 13
  residues processed: 192
  average time/residue: 0.6745
  time to fit residues: 136.6168
Evaluate side-chains
  178 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0060
   chunk 68 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 239 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.105834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.072780 restraints weight = 14754.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.98
r_work: 0.2816 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8913  Z= 0.154
  Angle     :  0.569   8.288  12119  Z= 0.291
  Chirality :  0.042   0.214   1372
  Planarity :  0.004   0.051   1529
  Dihedral  :  5.075  59.816   1230
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 18.16 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.26), residues: 1117
  helix:  2.41 (0.27), residues: 388
  sheet: -1.22 (0.29), residues: 276
  loop : -1.04 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  24 
 TYR   0.024   0.001   TYR S 235 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.017   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8911)
  covalent geometry    : angle       0.56930 (12117)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.21579 (    2)
  hydrogen bonds       : bond        0.03983 (  426)
  hydrogen bonds       : angle       4.59533 ( 1230)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 164
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8804 (mtp) cc_final: 0.8470 (mtm)
REVERT: A  298 GLU cc_start: 0.8815 (tt0) cc_final: 0.8512 (tt0)
REVERT: A  306 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8699 (mm110)
REVERT: B   16 ASN cc_start: 0.8711 (m-40) cc_final: 0.7927 (m-40)
REVERT: B   19 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8682 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8209 (mpt90) cc_final: 0.7868 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7984 (mtp85)
REVERT: B  260 GLU cc_start: 0.8269 (pt0) cc_final: 0.7919 (tt0)
REVERT: B  268 ASN cc_start: 0.8993 (m110) cc_final: 0.8790 (p0)
REVERT: G   31 SER cc_start: 0.8004 (t) cc_final: 0.7750 (m)
REVERT: G   42 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8148 (pp20)
REVERT: S   43 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8398 (mtmm)
REVERT: S   82 GLN cc_start: 0.8255 (tp40) cc_final: 0.7786 (tp-100)
REVERT: S  186 GLN cc_start: 0.8573 (mt0) cc_final: 0.8183 (tt0)
REVERT: S  235 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6726 (t80)
REVERT: S  244 LYS cc_start: 0.8846 (tttp) cc_final: 0.8563 (ttpp)
REVERT: R   85 ARG cc_start: 0.8424 (mtm110) cc_final: 0.7648 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8770 (m-40) cc_final: 0.8269 (t0)
REVERT: R  150 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8304 (mt-10)
REVERT: R  157 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8273 (mtpt)
REVERT: R  200 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8108 (mmtp)
REVERT: R  263 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7289 (tm-30)
REVERT: R  303 MET cc_start: 0.7364 (tpp) cc_final: 0.7088 (ttp)
  outliers start: 44
  outliers final: 20
  residues processed: 189
  average time/residue: 0.6603
  time to fit residues: 132.2045
Evaluate side-chains
  184 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  150 GLU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 252 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.103996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.070936 restraints weight = 14739.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 2.94
r_work: 0.2779 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8913  Z= 0.197
  Angle     :  0.612  10.377  12119  Z= 0.309
  Chirality :  0.043   0.244   1372
  Planarity :  0.004   0.050   1529
  Dihedral  :  4.818  40.893   1228
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.47 %
    Favored  : 76.81 %
  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:  0.24 (0.26), residues: 1117
  helix:  2.41 (0.26), residues: 387
  sheet: -1.12 (0.29), residues: 275
  loop : -0.95 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  24 
 TYR   0.026   0.002   TYR S 235 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.017   0.001   TRP R  59 
 HIS   0.004   0.001   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 8911)
  covalent geometry    : angle       0.61190 (12117)
  SS BOND              : bond        0.00259 (    1)
  SS BOND              : angle       0.21347 (    2)
  hydrogen bonds       : bond        0.04142 (  426)
  hydrogen bonds       : angle       4.60944 ( 1230)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8705 (mtp) cc_final: 0.8431 (mtm)
REVERT: A  298 GLU cc_start: 0.8819 (tt0) cc_final: 0.8514 (tt0)
REVERT: A  306 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8721 (mm110)
REVERT: A  354 PHE cc_start: 0.6140 (OUTLIER) cc_final: 0.4573 (m-10)
REVERT: B   16 ASN cc_start: 0.8715 (m-40) cc_final: 0.7887 (m-40)
REVERT: B   19 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8639 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8225 (mpt90) cc_final: 0.7836 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8045 (mtp85)
REVERT: B  215 GLU cc_start: 0.8030 (pt0) cc_final: 0.7659 (pt0)
REVERT: B  217 MET cc_start: 0.9060 (ptm) cc_final: 0.8464 (ptp)
REVERT: B  260 GLU cc_start: 0.8314 (pt0) cc_final: 0.7895 (tt0)
REVERT: G   31 SER cc_start: 0.8014 (t) cc_final: 0.7754 (m)
REVERT: G   42 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8231 (pp20)
REVERT: S   43 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8538 (mtmm)
REVERT: S   82 GLN cc_start: 0.8241 (tp40) cc_final: 0.7772 (tp-100)
REVERT: S  160 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7385 (mtp85)
REVERT: S  186 GLN cc_start: 0.8580 (mt0) cc_final: 0.8184 (tt0)
REVERT: S  235 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6777 (t80)
REVERT: S  244 LYS cc_start: 0.8851 (tttp) cc_final: 0.8563 (ttpp)
REVERT: R   85 ARG cc_start: 0.8461 (mtm110) cc_final: 0.7704 (mtm180)
REVERT: R  157 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8281 (mtpt)
REVERT: R  200 LYS cc_start: 0.8339 (mmtp) cc_final: 0.8057 (mmtp)
REVERT: R  263 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: R  303 MET cc_start: 0.7213 (tpp) cc_final: 0.7010 (ttp)
  outliers start: 34
  outliers final: 18
  residues processed: 187
  average time/residue: 0.6653
  time to fit residues: 131.3260
Evaluate side-chains
  181 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  167 LYS
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0570
   chunk 104 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0980
   chunk 28 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0670
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
S  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.107065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.074263 restraints weight = 14653.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 2.95
r_work: 0.2844 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8913  Z= 0.111
  Angle     :  0.581  10.382  12119  Z= 0.291
  Chirality :  0.041   0.200   1372
  Planarity :  0.004   0.052   1529
  Dihedral  :  4.620  40.965   1228
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.23 %
    Favored  : 75.38 %
  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:  0.40 (0.26), residues: 1117
  helix:  2.46 (0.26), residues: 388
  sheet: -0.92 (0.29), residues: 272
  loop : -0.89 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R  50 
 TYR   0.020   0.001   TYR S 235 
 PHE   0.011   0.001   PHE R 208 
 TRP   0.016   0.001   TRP R  59 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8911)
  covalent geometry    : angle       0.58097 (12117)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       0.23846 (    2)
  hydrogen bonds       : bond        0.03661 (  426)
  hydrogen bonds       : angle       4.47216 ( 1230)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 165
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7137 (mtm-85)
REVERT: A  247 MET cc_start: 0.8671 (mtp) cc_final: 0.8399 (mtm)
REVERT: A  298 GLU cc_start: 0.8802 (tt0) cc_final: 0.8465 (tt0)
REVERT: A  306 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8634 (mm110)
REVERT: B   16 ASN cc_start: 0.8725 (m-40) cc_final: 0.7926 (m-40)
REVERT: B   19 ARG cc_start: 0.8998 (ttp80) cc_final: 0.8660 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8164 (mpt90) cc_final: 0.7833 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8301 (mtp85) cc_final: 0.8015 (mtp85)
REVERT: B  215 GLU cc_start: 0.8121 (pt0) cc_final: 0.7496 (pt0)
REVERT: B  217 MET cc_start: 0.9033 (ptm) cc_final: 0.8443 (ptp)
REVERT: B  260 GLU cc_start: 0.8206 (pt0) cc_final: 0.7779 (tt0)
REVERT: B  268 ASN cc_start: 0.8984 (m110) cc_final: 0.8771 (p0)
REVERT: G   31 SER cc_start: 0.7987 (t) cc_final: 0.7739 (m)
REVERT: G   42 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8150 (pp20)
REVERT: S   43 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8407 (mtmm)
REVERT: S   82 GLN cc_start: 0.8236 (tp40) cc_final: 0.7732 (tp-100)
REVERT: S   87 ARG cc_start: 0.8654 (pmm-80) cc_final: 0.8411 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7392 (mtp85)
REVERT: S  186 GLN cc_start: 0.8552 (mt0) cc_final: 0.8120 (tt0)
REVERT: S  235 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6656 (t80)
REVERT: S  244 LYS cc_start: 0.8839 (tttp) cc_final: 0.8550 (ttpp)
REVERT: R   85 ARG cc_start: 0.8424 (mtm110) cc_final: 0.7669 (mtm180)
REVERT: R  113 ASN cc_start: 0.8710 (m-40) cc_final: 0.8053 (t0)
REVERT: R  157 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8265 (mtpt)
REVERT: R  200 LYS cc_start: 0.8367 (mmtp) cc_final: 0.8104 (mmtp)
REVERT: R  201 THR cc_start: 0.8663 (p) cc_final: 0.8315 (m)
REVERT: R  263 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7242 (tm-30)
REVERT: R  269 MET cc_start: 0.7582 (mmm) cc_final: 0.7319 (mmt)
REVERT: R  303 MET cc_start: 0.7045 (tpp) cc_final: 0.6637 (ttp)
  outliers start: 31
  outliers final: 13
  residues processed: 182
  average time/residue: 0.6333
  time to fit residues: 121.7153
Evaluate side-chains
  173 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 101 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 259 GLN
S 113 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.106213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.073395 restraints weight = 14542.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.93
r_work: 0.2829 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8913  Z= 0.138
  Angle     :  0.579  10.426  12119  Z= 0.293
  Chirality :  0.042   0.208   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.554  38.801   1228
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.21 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.26), residues: 1117
  helix:  2.50 (0.26), residues: 389
  sheet: -0.89 (0.29), residues: 274
  loop : -0.83 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R  50 
 TYR   0.024   0.001   TYR A 296 
 PHE   0.013   0.001   PHE R 208 
 TRP   0.015   0.001   TRP R  59 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8911)
  covalent geometry    : angle       0.57929 (12117)
  SS BOND              : bond        0.00297 (    1)
  SS BOND              : angle       0.21027 (    2)
  hydrogen bonds       : bond        0.03735 (  426)
  hydrogen bonds       : angle       4.44877 ( 1230)
  Misc. bond           : bond        0.00000 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7484 (ttm-80)
REVERT: A  247 MET cc_start: 0.8646 (mtp) cc_final: 0.8375 (mtm)
REVERT: A  298 GLU cc_start: 0.8795 (tt0) cc_final: 0.8437 (tt0)
REVERT: A  306 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8651 (mm110)
REVERT: B   16 ASN cc_start: 0.8757 (m-40) cc_final: 0.8086 (m-40)
REVERT: B   19 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8632 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8156 (mpt90) cc_final: 0.7816 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7951 (mmm-85)
REVERT: B  217 MET cc_start: 0.8968 (ptm) cc_final: 0.8299 (ptm)
REVERT: B  260 GLU cc_start: 0.8241 (pt0) cc_final: 0.7818 (tt0)
REVERT: B  268 ASN cc_start: 0.8980 (m110) cc_final: 0.8764 (p0)
REVERT: G   17 GLU cc_start: 0.9234 (tp30) cc_final: 0.8817 (mp0)
REVERT: G   31 SER cc_start: 0.7999 (t) cc_final: 0.7750 (m)
REVERT: G   42 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8203 (pp20)
REVERT: S   43 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8445 (mtmm)
REVERT: S   82 GLN cc_start: 0.8301 (tp40) cc_final: 0.7826 (tp-100)
REVERT: S   87 ARG cc_start: 0.8689 (pmm-80) cc_final: 0.8421 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7463 (mtp85)
REVERT: S  186 GLN cc_start: 0.8553 (mt0) cc_final: 0.8126 (tt0)
REVERT: S  235 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6713 (t80)
REVERT: S  244 LYS cc_start: 0.8857 (tttp) cc_final: 0.8569 (ttpp)
REVERT: R   85 ARG cc_start: 0.8412 (mtm110) cc_final: 0.7692 (mtm180)
REVERT: R  113 ASN cc_start: 0.8672 (m-40) cc_final: 0.8030 (t0)
REVERT: R  157 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8258 (mtpt)
REVERT: R  200 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8099 (mmtp)
REVERT: R  201 THR cc_start: 0.8694 (p) cc_final: 0.8358 (m)
REVERT: R  263 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: R  269 MET cc_start: 0.7582 (mmm) cc_final: 0.7377 (mmt)
REVERT: R  303 MET cc_start: 0.6960 (tpp) cc_final: 0.6638 (ttp)
  outliers start: 25
  outliers final: 18
  residues processed: 176
  average time/residue: 0.6926
  time to fit residues: 128.6632
Evaluate side-chains
  179 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  313 SER
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0050
   chunk 79 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 259 GLN
S  39 GLN
S 113 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.107076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.074230 restraints weight = 14621.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.96
r_work: 0.2844 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8913  Z= 0.124
  Angle     :  0.578  11.322  12119  Z= 0.290
  Chirality :  0.041   0.198   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.509  37.994   1228
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.99 %
    Favored  : 75.27 %
  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:  0.57 (0.26), residues: 1117
  helix:  2.56 (0.26), residues: 389
  sheet: -0.79 (0.29), residues: 272
  loop : -0.78 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  21 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.012   0.001   PHE R  69 
 TRP   0.014   0.001   TRP R  59 
 HIS   0.002   0.000   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8911)
  covalent geometry    : angle       0.57802 (12117)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       0.10129 (    2)
  hydrogen bonds       : bond        0.03628 (  426)
  hydrogen bonds       : angle       4.42299 ( 1230)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8668 (mtp) cc_final: 0.8392 (mtm)
REVERT: A  275 GLU cc_start: 0.8944 (tt0) cc_final: 0.8685 (tt0)
REVERT: A  298 GLU cc_start: 0.8784 (tt0) cc_final: 0.8422 (tt0)
REVERT: A  306 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8642 (mm110)
REVERT: B   16 ASN cc_start: 0.8734 (m-40) cc_final: 0.8054 (m-40)
REVERT: B   19 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8603 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8144 (mpt90) cc_final: 0.7814 (mtm-85)
REVERT: B  217 MET cc_start: 0.9062 (ptm) cc_final: 0.8435 (ppp)
REVERT: B  260 GLU cc_start: 0.8209 (pt0) cc_final: 0.7798 (tt0)
REVERT: B  268 ASN cc_start: 0.8964 (m110) cc_final: 0.8749 (p0)
REVERT: G   31 SER cc_start: 0.7999 (t) cc_final: 0.7754 (m)
REVERT: G   42 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8183 (pp20)
REVERT: S   43 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8430 (mtmm)
REVERT: S   82 GLN cc_start: 0.8316 (tp40) cc_final: 0.7843 (tp-100)
REVERT: S   87 ARG cc_start: 0.8707 (pmm-80) cc_final: 0.8434 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7460 (mtp85)
REVERT: S  186 GLN cc_start: 0.8550 (mt0) cc_final: 0.8113 (tt0)
REVERT: S  235 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6700 (t80)
REVERT: S  244 LYS cc_start: 0.8864 (tttp) cc_final: 0.8578 (ttpp)
REVERT: R   85 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7689 (mtm180)
REVERT: R  113 ASN cc_start: 0.8631 (m-40) cc_final: 0.7990 (t0)
REVERT: R  157 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8246 (mtpt)
REVERT: R  200 LYS cc_start: 0.8459 (mmtp) cc_final: 0.7577 (mmmm)
REVERT: R  201 THR cc_start: 0.8671 (p) cc_final: 0.8361 (m)
REVERT: R  247 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7852 (ttp80)
REVERT: R  263 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7326 (tm-30)
REVERT: R  269 MET cc_start: 0.7565 (mmm) cc_final: 0.7342 (mmt)
REVERT: R  303 MET cc_start: 0.6751 (tpp) cc_final: 0.6493 (ttp)
REVERT: R  325 MET cc_start: 0.8234 (mmt) cc_final: 0.7874 (mmm)
  outliers start: 25
  outliers final: 16
  residues processed: 177
  average time/residue: 0.6885
  time to fit residues: 128.7117
Evaluate side-chains
  180 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  247 ARG
Chi-restraints excluded: chain R residue  313 SER
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 76 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0170
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
S  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.107105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.074666 restraints weight = 14710.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.97
r_work: 0.2849 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8913  Z= 0.120
  Angle     :  0.588  11.965  12119  Z= 0.294
  Chirality :  0.042   0.192   1372
  Planarity :  0.004   0.055   1529
  Dihedral  :  4.456  37.522   1228
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.65 %
    Favored  : 74.62 %
  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:  0.59 (0.26), residues: 1117
  helix:  2.54 (0.26), residues: 392
  sheet: -0.77 (0.29), residues: 272
  loop : -0.75 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 214 
 TYR   0.026   0.001   TYR A 296 
 PHE   0.012   0.001   PHE R  69 
 TRP   0.014   0.001   TRP R  59 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8911)
  covalent geometry    : angle       0.58785 (12117)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       0.09578 (    2)
  hydrogen bonds       : bond        0.03573 (  426)
  hydrogen bonds       : angle       4.39606 ( 1230)
  Misc. bond           : bond        0.00119 (    1)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8694 (mtp) cc_final: 0.8411 (mtm)
REVERT: A  298 GLU cc_start: 0.8780 (tt0) cc_final: 0.8425 (tt0)
REVERT: A  306 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8664 (mm110)
REVERT: A  315 ASP cc_start: 0.9257 (p0) cc_final: 0.8906 (p0)
REVERT: B   16 ASN cc_start: 0.8771 (m-40) cc_final: 0.8106 (m-40)
REVERT: B   19 ARG cc_start: 0.8953 (ttp80) cc_final: 0.8561 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8136 (mpt90) cc_final: 0.7814 (mtm-85)
REVERT: B  197 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8221 (mmm-85)
REVERT: B  214 ARG cc_start: 0.8924 (mtt90) cc_final: 0.8616 (mmt90)
REVERT: B  215 GLU cc_start: 0.8198 (pt0) cc_final: 0.7631 (pp20)
REVERT: B  217 MET cc_start: 0.9043 (ptm) cc_final: 0.8503 (ppp)
REVERT: B  260 GLU cc_start: 0.8204 (pt0) cc_final: 0.7805 (tt0)
REVERT: B  268 ASN cc_start: 0.8944 (m110) cc_final: 0.8735 (p0)
REVERT: G   21 MET cc_start: 0.9127 (mmm) cc_final: 0.8747 (mmm)
REVERT: G   31 SER cc_start: 0.8002 (t) cc_final: 0.7756 (m)
REVERT: G   42 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8141 (pp20)
REVERT: S   43 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8431 (mtmm)
REVERT: S   82 GLN cc_start: 0.8408 (tp40) cc_final: 0.7919 (tp-100)
REVERT: S   87 ARG cc_start: 0.8729 (pmm-80) cc_final: 0.8452 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7493 (mtp85)
REVERT: S  186 GLN cc_start: 0.8562 (mt0) cc_final: 0.8130 (tt0)
REVERT: S  235 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6681 (t80)
REVERT: S  244 LYS cc_start: 0.8871 (tttp) cc_final: 0.8590 (ttpp)
REVERT: R   85 ARG cc_start: 0.8415 (mtm110) cc_final: 0.7691 (mtm180)
REVERT: R  113 ASN cc_start: 0.8621 (m-40) cc_final: 0.7988 (t0)
REVERT: R  157 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8217 (mtpt)
REVERT: R  200 LYS cc_start: 0.8488 (mmtp) cc_final: 0.7609 (mmmm)
REVERT: R  201 THR cc_start: 0.8646 (p) cc_final: 0.8351 (m)
REVERT: R  247 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7862 (ttp-170)
REVERT: R  263 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7292 (tm-30)
REVERT: R  325 MET cc_start: 0.8271 (mmt) cc_final: 0.7949 (mmm)
  outliers start: 25
  outliers final: 13
  residues processed: 184
  average time/residue: 0.6832
  time to fit residues: 132.7897
Evaluate side-chains
  181 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   43 LYS
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  223 ASP
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  247 ARG
Chi-restraints excluded: chain R residue  315 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0170
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  13 GLN
B 259 GLN
S  39 GLN
S 113 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.106863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.074449 restraints weight = 14670.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.97
r_work: 0.2848 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8913  Z= 0.129
  Angle     :  0.592  11.765  12119  Z= 0.296
  Chirality :  0.042   0.193   1372
  Planarity :  0.004   0.055   1529
  Dihedral  :  4.384  35.928   1227
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.54 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.26), residues: 1117
  helix:  2.53 (0.26), residues: 391
  sheet: -0.78 (0.29), residues: 272
  loop : -0.74 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 214 
 TYR   0.019   0.001   TYR S 235 
 PHE   0.012   0.001   PHE R 208 
 TRP   0.015   0.001   TRP R  59 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8911)
  covalent geometry    : angle       0.59202 (12117)
  SS BOND              : bond        0.00282 (    1)
  SS BOND              : angle       0.06014 (    2)
  hydrogen bonds       : bond        0.03597 (  426)
  hydrogen bonds       : angle       4.38600 ( 1230)
  Misc. bond           : bond        0.00145 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4183.45 seconds
wall clock time: 72 minutes 4.99 seconds (4324.99 seconds total)