Starting phenix.real_space_refine
on Sat Jul 26 17:45:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y01_38800/07_2025/8y01_38800_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y01_38800/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y01_38800/07_2025/8y01_38800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y01_38800/07_2025/8y01_38800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y01_38800/07_2025/8y01_38800_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y01_38800/07_2025/8y01_38800_neut.cif"
  }
  resolution = 2.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7}
          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: {'PHE:plan': 1, 'ARG:plan': 1, 'HIS: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: 5.92, per 1000 atoms: 0.68
  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: 3.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.00
  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: 2.67

  Time building geometry restraints manager: 2.94 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:             31.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     24.570
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:13.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.720
-------------------------------------------------------------------------------
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 : 12.18
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.044   0.003   TRP S 111 
 HIS   0.022   0.003   HIS S  35 
 PHE   0.035   0.004   PHE S 177 
 TYR   0.041   0.004   TYR S  94 
 ARG   0.007   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19514 (  426)
  hydrogen bonds       : angle       7.11447 ( 1230)
  SS BOND              : bond        0.44298 (    1)
  SS BOND              : angle       4.57100 (    2)
  covalent geometry    : bond        0.01205 ( 8911)
  covalent geometry    : angle       1.36091 (12117)
  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  : 0.975 
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: 1.2840
  time to fit residues: 327.8337
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  : 1.136 
-------------------------------------------------------------------------------
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 92 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.107209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.073980 restraints weight = 14437.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.96
r_work: 0.2837 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8913  Z= 0.159
  Angle     :  0.634   8.908  12119  Z= 0.330
  Chirality :  0.044   0.249   1372
  Planarity :  0.005   0.055   1529
  Dihedral  :  6.420  57.008   1245
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 12.36 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1117
  helix:  1.81 (0.26), residues: 383
  sheet: -1.66 (0.29), residues: 278
  loop : -1.48 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S 111 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.016   0.002   PHE R 208 
 TYR   0.021   0.002   TYR S 235 
 ARG   0.006   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04992 (  426)
  hydrogen bonds       : angle       5.07471 ( 1230)
  SS BOND              : bond        0.00659 (    1)
  SS BOND              : angle       0.56751 (    2)
  covalent geometry    : bond        0.00345 ( 8911)
  covalent geometry    : angle       0.63449 (12117)
  Misc. bond           : bond        0.00029 (    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
  227 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8810 (mtp) cc_final: 0.8605 (ttm)
REVERT: A  298 GLU cc_start: 0.8874 (tt0) cc_final: 0.8634 (tt0)
REVERT: A  306 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8709 (mm110)
REVERT: A  354 PHE cc_start: 0.4917 (OUTLIER) cc_final: 0.4189 (m-10)
REVERT: B   16 ASN cc_start: 0.8706 (m-40) cc_final: 0.8282 (m-40)
REVERT: B   19 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8719 (tmm-80)
REVERT: B   22 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8674 (mtt180)
REVERT: B  215 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7178 (pt0)
REVERT: G   31 SER cc_start: 0.8069 (t) cc_final: 0.7670 (m)
REVERT: G   42 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8096 (pp20)
REVERT: S   82 GLN cc_start: 0.8298 (tp40) cc_final: 0.7892 (tp-100)
REVERT: S  186 GLN cc_start: 0.8521 (mt0) cc_final: 0.8132 (tt0)
REVERT: S  235 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6759 (t80)
REVERT: S  244 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8516 (ttpp)
REVERT: R  113 ASN cc_start: 0.8928 (m-40) cc_final: 0.8471 (t0)
REVERT: R  157 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8279 (mtpt)
REVERT: R  258 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.7241 (t)
REVERT: R  263 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7205 (tm-30)
REVERT: R  265 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7370 (tt0)
  outliers start: 46
  outliers final: 9
  residues processed: 207
  average time/residue: 1.3563
  time to fit residues: 297.0589
Evaluate side-chains
  174 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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  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 S residue  235 TYR
Chi-restraints excluded: chain S residue  244 LYS
Chi-restraints excluded: chain R residue  107 SER
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 64 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  89 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.106733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.073822 restraints weight = 14785.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.98
r_work: 0.2835 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8913  Z= 0.133
  Angle     :  0.578   8.882  12119  Z= 0.296
  Chirality :  0.042   0.238   1372
  Planarity :  0.004   0.050   1529
  Dihedral  :  5.692  59.549   1235
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.63 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1117
  helix:  2.21 (0.26), residues: 385
  sheet: -1.43 (0.29), residues: 277
  loop : -1.33 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S 111 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.016   0.001   PHE R 164 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.009   0.001   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04250 (  426)
  hydrogen bonds       : angle       4.74397 ( 1230)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       0.21267 (    2)
  covalent geometry    : bond        0.00292 ( 8911)
  covalent geometry    : angle       0.57835 (12117)
  Misc. bond           : bond        0.00007 (    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: 37
    poor density    : 170
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8800 (mtp) cc_final: 0.8412 (mtm)
REVERT: A  298 GLU cc_start: 0.8912 (tt0) cc_final: 0.8656 (tt0)
REVERT: A  306 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8633 (mm110)
REVERT: A  337 ASP cc_start: 0.8151 (m-30) cc_final: 0.7920 (m-30)
REVERT: A  354 PHE cc_start: 0.4964 (OUTLIER) cc_final: 0.4338 (m-10)
REVERT: B   16 ASN cc_start: 0.8654 (m-40) cc_final: 0.8123 (m-40)
REVERT: B   19 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8739 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8250 (mpt90) cc_final: 0.7786 (mpp80)
REVERT: B  197 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7918 (mtp85)
REVERT: B  217 MET cc_start: 0.9063 (ptp) cc_final: 0.8554 (pmt)
REVERT: G   31 SER cc_start: 0.8018 (t) cc_final: 0.7790 (m)
REVERT: G   42 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8166 (pp20)
REVERT: S   82 GLN cc_start: 0.8261 (tp40) cc_final: 0.7809 (tp-100)
REVERT: S   87 ARG cc_start: 0.8828 (ptp-170) cc_final: 0.8603 (pmm-80)
REVERT: S  186 GLN cc_start: 0.8543 (mt0) cc_final: 0.8219 (tt0)
REVERT: S  244 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8552 (ttpp)
REVERT: R   85 ARG cc_start: 0.8500 (mtm110) cc_final: 0.7803 (mtm-85)
REVERT: R  113 ASN cc_start: 0.8911 (m-40) cc_final: 0.8415 (t0)
REVERT: R  157 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8274 (mtpt)
REVERT: R  200 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7960 (mmtp)
REVERT: R  263 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7335 (tm-30)
REVERT: R  265 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7289 (tt0)
  outliers start: 37
  outliers final: 14
  residues processed: 188
  average time/residue: 1.3314
  time to fit residues: 264.6889
Evaluate side-chains
  176 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  244 LYS
Chi-restraints excluded: chain R residue  107 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 99 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  75 GLN
B  88 ASN
B 239 ASN
B 259 GLN
B 266 HIS
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 335 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.106963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.074002 restraints weight = 14584.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.96
r_work: 0.2842 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
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 = 0.61   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 = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8913  Z= 0.137
  Angle     :  0.569   8.689  12119  Z= 0.289
  Chirality :  0.042   0.217   1372
  Planarity :  0.004   0.049   1529
  Dihedral  :  5.093  58.287   1230
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 17.51 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1117
  helix:  2.36 (0.26), residues: 386
  sheet: -1.33 (0.28), residues: 277
  loop : -1.17 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R  59 
 HIS   0.002   0.001   HIS S 232 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.007   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04004 (  426)
  hydrogen bonds       : angle       4.63238 ( 1230)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       0.22317 (    2)
  covalent geometry    : bond        0.00307 ( 8911)
  covalent geometry    : angle       0.56949 (12117)
  Misc. bond           : bond        0.00013 (    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
  212 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 174
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8296 (mtpt)
REVERT: A  247 MET cc_start: 0.8856 (mtp) cc_final: 0.8431 (mtm)
REVERT: A  298 GLU cc_start: 0.8930 (tt0) cc_final: 0.8631 (tt0)
REVERT: A  306 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8607 (mm110)
REVERT: B   16 ASN cc_start: 0.8698 (m-40) cc_final: 0.7971 (m-40)
REVERT: B   19 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8704 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8227 (mpt90) cc_final: 0.7756 (mpp80)
REVERT: B  197 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7926 (mmm-85)
REVERT: B  260 GLU cc_start: 0.8184 (pt0) cc_final: 0.7738 (tt0)
REVERT: G   31 SER cc_start: 0.7957 (t) cc_final: 0.7735 (m)
REVERT: G   42 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8086 (pp20)
REVERT: S   43 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8349 (mtmm)
REVERT: S   82 GLN cc_start: 0.8253 (tp40) cc_final: 0.7779 (tp-100)
REVERT: S   87 ARG cc_start: 0.8808 (ptp-170) cc_final: 0.8592 (pmm-80)
REVERT: S  186 GLN cc_start: 0.8512 (mt0) cc_final: 0.8135 (tt0)
REVERT: S  235 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6759 (t80)
REVERT: S  244 LYS cc_start: 0.8824 (tttp) cc_final: 0.8534 (ttpp)
REVERT: R   85 ARG cc_start: 0.8486 (mtm110) cc_final: 0.7617 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8803 (m-40) cc_final: 0.8319 (t0)
REVERT: R  157 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8279 (mtpt)
REVERT: R  200 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8074 (mmtp)
REVERT: R  263 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: R  303 MET cc_start: 0.7500 (tpp) cc_final: 0.7166 (ttp)
  outliers start: 38
  outliers final: 17
  residues processed: 195
  average time/residue: 1.2761
  time to fit residues: 264.4403
Evaluate side-chains
  183 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
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  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  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 100 optimal weight:    0.4980
   chunk 78 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0670
   chunk 42 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R  44 ASN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.107582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.074797 restraints weight = 14605.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.95
r_work: 0.2853 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8913  Z= 0.122
  Angle     :  0.551   8.055  12119  Z= 0.281
  Chirality :  0.041   0.208   1372
  Planarity :  0.004   0.052   1529
  Dihedral  :  4.937  59.269   1230
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 18.27 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.26), residues: 1117
  helix:  2.38 (0.26), residues: 389
  sheet: -1.21 (0.28), residues: 276
  loop : -1.06 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.008   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  426)
  hydrogen bonds       : angle       4.54304 ( 1230)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       0.11536 (    2)
  covalent geometry    : bond        0.00273 ( 8911)
  covalent geometry    : angle       0.55065 (12117)
  Misc. bond           : bond        0.00002 (    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
  206 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8841 (mtp) cc_final: 0.8491 (mtm)
REVERT: A  298 GLU cc_start: 0.8924 (tt0) cc_final: 0.8594 (tt0)
REVERT: A  306 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8695 (mm110)
REVERT: B   16 ASN cc_start: 0.8727 (m-40) cc_final: 0.7928 (m-40)
REVERT: B   19 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8713 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8194 (mpt90) cc_final: 0.7729 (mpp80)
REVERT: B  215 GLU cc_start: 0.7598 (pt0) cc_final: 0.7382 (pt0)
REVERT: B  217 MET cc_start: 0.9011 (ptp) cc_final: 0.8677 (ptp)
REVERT: B  260 GLU cc_start: 0.8206 (pt0) cc_final: 0.7756 (tt0)
REVERT: G   17 GLU cc_start: 0.9233 (tp30) cc_final: 0.8873 (mp0)
REVERT: G   31 SER cc_start: 0.7986 (t) cc_final: 0.7761 (m)
REVERT: G   42 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8163 (pp20)
REVERT: S   43 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8354 (mtmm)
REVERT: S   82 GLN cc_start: 0.8242 (tp40) cc_final: 0.7744 (tp-100)
REVERT: S  160 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7360 (mtp85)
REVERT: S  186 GLN cc_start: 0.8542 (mt0) cc_final: 0.8169 (tt0)
REVERT: S  235 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6698 (t80)
REVERT: S  244 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8552 (ttpp)
REVERT: R   85 ARG cc_start: 0.8402 (mtm110) cc_final: 0.7634 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8756 (m-40) cc_final: 0.8197 (t0)
REVERT: R  150 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (mt-10)
REVERT: R  157 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8267 (mtpt)
REVERT: R  200 LYS cc_start: 0.8354 (mmtp) cc_final: 0.8135 (mmtp)
REVERT: R  201 THR cc_start: 0.8588 (p) cc_final: 0.8319 (m)
REVERT: R  263 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7298 (tm-30)
REVERT: R  303 MET cc_start: 0.7387 (tpp) cc_final: 0.7112 (ttp)
REVERT: R  325 MET cc_start: 0.8252 (mmt) cc_final: 0.7929 (mmm)
  outliers start: 38
  outliers final: 17
  residues processed: 185
  average time/residue: 1.2873
  time to fit residues: 252.5851
Evaluate side-chains
  182 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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  270 ILE
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 S residue  235 TYR
Chi-restraints excluded: chain S residue  244 LYS
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  150 GLU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.106271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.073197 restraints weight = 14496.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 2.95
r_work: 0.2825 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8913  Z= 0.154
  Angle     :  0.576   9.674  12119  Z= 0.291
  Chirality :  0.042   0.220   1372
  Planarity :  0.004   0.055   1529
  Dihedral  :  4.909  59.350   1230
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 18.93 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1117
  helix:  2.48 (0.26), residues: 388
  sheet: -1.12 (0.28), residues: 276
  loop : -0.98 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.024   0.002   PHE R 208 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.006   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  426)
  hydrogen bonds       : angle       4.52676 ( 1230)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       0.11071 (    2)
  covalent geometry    : bond        0.00352 ( 8911)
  covalent geometry    : angle       0.57649 (12117)
  Misc. bond           : bond        0.00008 (    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
  208 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 GLU cc_start: 0.8940 (tt0) cc_final: 0.8611 (tt0)
REVERT: A  306 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8711 (mm110)
REVERT: A  354 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.3588 (m-10)
REVERT: B   16 ASN cc_start: 0.8724 (m-40) cc_final: 0.7922 (m-40)
REVERT: B   19 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8675 (tmm-80)
REVERT: B   44 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8182 (mp10)
REVERT: B   46 ARG cc_start: 0.8199 (mpt90) cc_final: 0.7837 (mtm-85)
REVERT: B  217 MET cc_start: 0.8990 (ptp) cc_final: 0.8594 (ptm)
REVERT: B  260 GLU cc_start: 0.8260 (pt0) cc_final: 0.7805 (tt0)
REVERT: G   31 SER cc_start: 0.7986 (t) cc_final: 0.7756 (m)
REVERT: G   42 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8120 (pp20)
REVERT: S   43 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8383 (mtmm)
REVERT: S   82 GLN cc_start: 0.8246 (tp40) cc_final: 0.7748 (tp-100)
REVERT: S  160 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7311 (mtp85)
REVERT: S  186 GLN cc_start: 0.8565 (mt0) cc_final: 0.8176 (tt0)
REVERT: S  235 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6699 (t80)
REVERT: S  244 LYS cc_start: 0.8845 (tttp) cc_final: 0.8563 (ttpp)
REVERT: R   85 ARG cc_start: 0.8394 (mtm110) cc_final: 0.7633 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8768 (m-40) cc_final: 0.8192 (t0)
REVERT: R  157 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8266 (mtpt)
REVERT: R  200 LYS cc_start: 0.8312 (mmtp) cc_final: 0.8105 (mmtp)
REVERT: R  201 THR cc_start: 0.8615 (p) cc_final: 0.8347 (m)
REVERT: R  263 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7272 (tm-30)
REVERT: R  269 MET cc_start: 0.7584 (mmm) cc_final: 0.7376 (mmt)
REVERT: R  303 MET cc_start: 0.7236 (tpp) cc_final: 0.7011 (ttp)
REVERT: R  325 MET cc_start: 0.8312 (mmt) cc_final: 0.8002 (mmm)
  outliers start: 42
  outliers final: 23
  residues processed: 192
  average time/residue: 1.2548
  time to fit residues: 255.9095
Evaluate side-chains
  189 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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 A residue  354 PHE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 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 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   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  278 CYS
Chi-restraints excluded: chain R residue  313 SER
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 15 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   overall best weight:    1.7186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.103888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.070844 restraints weight = 14829.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.94
r_work: 0.2781 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8913  Z= 0.213
  Angle     :  0.613   8.924  12119  Z= 0.313
  Chirality :  0.044   0.246   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.734  37.119   1228
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.13 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1117
  helix:  2.42 (0.26), residues: 388
  sheet: -1.10 (0.28), residues: 277
  loop : -0.96 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.017   0.002   PHE R 279 
 TYR   0.026   0.002   TYR S 235 
 ARG   0.008   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  426)
  hydrogen bonds       : angle       4.59066 ( 1230)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.22915 (    2)
  covalent geometry    : bond        0.00497 ( 8911)
  covalent geometry    : angle       0.61296 (12117)
  Misc. bond           : bond        0.00055 (    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
  198 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8818 (mtp) cc_final: 0.8445 (mtm)
REVERT: A  298 GLU cc_start: 0.8931 (tt0) cc_final: 0.8592 (tt0)
REVERT: A  306 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8729 (mm110)
REVERT: B   16 ASN cc_start: 0.8728 (m-40) cc_final: 0.7903 (m-40)
REVERT: B   19 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8633 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8219 (mpt90) cc_final: 0.7872 (mtm-85)
REVERT: B  214 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8623 (mmt90)
REVERT: B  217 MET cc_start: 0.9056 (ptp) cc_final: 0.8491 (ptp)
REVERT: B  260 GLU cc_start: 0.8353 (pt0) cc_final: 0.7848 (tt0)
REVERT: G   31 SER cc_start: 0.8014 (t) cc_final: 0.7766 (m)
REVERT: G   42 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8190 (pp20)
REVERT: S   43 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8458 (mtmm)
REVERT: S   82 GLN cc_start: 0.8216 (tp40) cc_final: 0.7737 (tp-100)
REVERT: S   87 ARG cc_start: 0.8675 (pmm-80) cc_final: 0.8415 (pmm-80)
REVERT: S  160 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7330 (mtp85)
REVERT: S  186 GLN cc_start: 0.8584 (mt0) cc_final: 0.8187 (tt0)
REVERT: S  235 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6759 (t80)
REVERT: S  244 LYS cc_start: 0.8857 (tttp) cc_final: 0.8565 (ttpp)
REVERT: R   85 ARG cc_start: 0.8421 (mtm110) cc_final: 0.7606 (mtt-85)
REVERT: R  157 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (mtpt)
REVERT: R  200 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8113 (mmtp)
REVERT: R  201 THR cc_start: 0.8637 (p) cc_final: 0.8356 (m)
REVERT: R  263 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: R  303 MET cc_start: 0.7105 (tpp) cc_final: 0.6720 (ttp)
REVERT: R  325 MET cc_start: 0.8366 (mmt) cc_final: 0.8015 (mmm)
  outliers start: 36
  outliers final: 18
  residues processed: 183
  average time/residue: 1.4301
  time to fit residues: 277.9106
Evaluate side-chains
  177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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  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 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  144 LEU
Chi-restraints excluded: chain R residue  157 LYS
Chi-restraints excluded: chain R residue  167 LYS
Chi-restraints excluded: chain R residue  278 CYS
Chi-restraints excluded: chain R residue  312 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 22 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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  39 GLN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.106587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.073792 restraints weight = 14645.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.94
r_work: 0.2835 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3368

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= 0.129
  Angle     :  0.581  11.122  12119  Z= 0.295
  Chirality :  0.042   0.206   1372
  Planarity :  0.004   0.054   1529
  Dihedral  :  4.582  37.282   1228
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1117
  helix:  2.50 (0.26), residues: 388
  sheet: -0.92 (0.29), residues: 274
  loop : -0.86 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.017   0.001   PHE R 279 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.013   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (  426)
  hydrogen bonds       : angle       4.48509 ( 1230)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.18425 (    2)
  covalent geometry    : bond        0.00294 ( 8911)
  covalent geometry    : angle       0.58065 (12117)
  Misc. bond           : bond        0.00011 (    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
  197 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 167
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8801 (mtp) cc_final: 0.8455 (mtm)
REVERT: A  298 GLU cc_start: 0.8931 (tt0) cc_final: 0.8598 (tt0)
REVERT: A  306 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8641 (mm110)
REVERT: B   16 ASN cc_start: 0.8722 (m-40) cc_final: 0.8155 (m-40)
REVERT: B   19 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8601 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8150 (mpt90) cc_final: 0.7831 (mtm-85)
REVERT: B  214 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8694 (mmt90)
REVERT: B  215 GLU cc_start: 0.7958 (pt0) cc_final: 0.7572 (pt0)
REVERT: B  260 GLU cc_start: 0.8242 (pt0) cc_final: 0.7793 (tt0)
REVERT: G   17 GLU cc_start: 0.9211 (tp30) cc_final: 0.8852 (mp0)
REVERT: G   31 SER cc_start: 0.8000 (t) cc_final: 0.7764 (m)
REVERT: G   42 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8168 (pp20)
REVERT: S   43 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8380 (mtmm)
REVERT: S   82 GLN cc_start: 0.8224 (tp40) cc_final: 0.7737 (tp-100)
REVERT: S   87 ARG cc_start: 0.8715 (pmm-80) cc_final: 0.8449 (pmm-80)
REVERT: S  160 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7366 (mtp85)
REVERT: S  186 GLN cc_start: 0.8541 (mt0) cc_final: 0.8100 (tt0)
REVERT: S  219 LEU cc_start: 0.9357 (mt) cc_final: 0.9156 (mm)
REVERT: S  235 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6612 (t80)
REVERT: S  244 LYS cc_start: 0.8849 (tttp) cc_final: 0.8558 (ttpp)
REVERT: R   85 ARG cc_start: 0.8407 (mtm110) cc_final: 0.7631 (mtt-85)
REVERT: R  113 ASN cc_start: 0.8667 (m-40) cc_final: 0.7993 (t0)
REVERT: R  157 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8251 (mtpt)
REVERT: R  200 LYS cc_start: 0.8403 (mmtp) cc_final: 0.8078 (mmtp)
REVERT: R  201 THR cc_start: 0.8642 (p) cc_final: 0.8282 (m)
REVERT: R  263 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7274 (tm-30)
REVERT: R  303 MET cc_start: 0.6983 (tpp) cc_final: 0.6651 (ttp)
  outliers start: 30
  outliers final: 15
  residues processed: 185
  average time/residue: 1.4631
  time to fit residues: 286.9304
Evaluate side-chains
  182 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
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  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 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  278 CYS
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 3 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    5.9990
   chunk 82 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0070
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.107074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.074783 restraints weight = 14657.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.95
r_work: 0.2854 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    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 = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3497

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= 0.120
  Angle     :  0.580  11.468  12119  Z= 0.293
  Chirality :  0.042   0.197   1372
  Planarity :  0.004   0.055   1529
  Dihedral  :  4.485  39.394   1228
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 22.21 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1117
  helix:  2.48 (0.26), residues: 390
  sheet: -0.82 (0.29), residues: 274
  loop : -0.84 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.016   0.001   PHE R 279 
 TYR   0.018   0.001   TYR S 235 
 ARG   0.011   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  426)
  hydrogen bonds       : angle       4.40487 ( 1230)
  SS BOND              : bond        0.00282 (    1)
  SS BOND              : angle       0.13699 (    2)
  covalent geometry    : bond        0.00269 ( 8911)
  covalent geometry    : angle       0.57981 (12117)
  Misc. bond           : bond        0.00084 (    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
  192 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8784 (mtp) cc_final: 0.8450 (mtm)
REVERT: A  298 GLU cc_start: 0.8899 (tt0) cc_final: 0.8548 (tt0)
REVERT: A  306 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8665 (mm110)
REVERT: B   16 ASN cc_start: 0.8757 (m-40) cc_final: 0.8149 (m-40)
REVERT: B   19 ARG cc_start: 0.8957 (ttp80) cc_final: 0.8551 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8134 (mpt90) cc_final: 0.7829 (mtm-85)
REVERT: B  214 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8694 (mmt90)
REVERT: B  260 GLU cc_start: 0.8208 (pt0) cc_final: 0.7773 (tt0)
REVERT: G   31 SER cc_start: 0.8021 (t) cc_final: 0.7797 (m)
REVERT: G   42 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8134 (pp20)
REVERT: S   43 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8390 (mtmm)
REVERT: S   82 GLN cc_start: 0.8243 (tp40) cc_final: 0.7727 (tp-100)
REVERT: S   87 ARG cc_start: 0.8733 (pmm-80) cc_final: 0.8460 (pmm-80)
REVERT: S  160 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7360 (mtp85)
REVERT: S  186 GLN cc_start: 0.8548 (mt0) cc_final: 0.8130 (tt0)
REVERT: S  235 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6673 (t80)
REVERT: S  244 LYS cc_start: 0.8870 (tttp) cc_final: 0.8584 (ttpp)
REVERT: R   85 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7643 (mtm180)
REVERT: R  113 ASN cc_start: 0.8632 (m-40) cc_final: 0.7992 (t0)
REVERT: R  157 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8232 (mtpt)
REVERT: R  200 LYS cc_start: 0.8464 (mmtp) cc_final: 0.7563 (mmmm)
REVERT: R  201 THR cc_start: 0.8677 (p) cc_final: 0.8348 (m)
REVERT: R  263 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: R  303 MET cc_start: 0.6870 (tpp) cc_final: 0.6568 (ttp)
  outliers start: 21
  outliers final: 12
  residues processed: 184
  average time/residue: 1.5667
  time to fit residues: 306.2084
Evaluate side-chains
  177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 162
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
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 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  157 LYS
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 42 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0570
   chunk 101 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B 259 GLN
S 113 GLN
R  44 ASN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.106945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.074583 restraints weight = 14691.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.95
r_work: 0.2849 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3563

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= 0.127
  Angle     :  0.589  11.889  12119  Z= 0.295
  Chirality :  0.042   0.197   1372
  Planarity :  0.004   0.055   1529
  Dihedral  :  4.393  35.070   1227
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.43 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.26), residues: 1117
  helix:  2.51 (0.26), residues: 392
  sheet: -0.78 (0.29), residues: 274
  loop : -0.83 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R 279 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.011   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03594 (  426)
  hydrogen bonds       : angle       4.37831 ( 1230)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       0.02781 (    2)
  covalent geometry    : bond        0.00288 ( 8911)
  covalent geometry    : angle       0.58943 (12117)
  Misc. bond           : bond        0.00123 (    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
  191 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.8853 (mtp) cc_final: 0.8504 (mtm)
REVERT: A  275 GLU cc_start: 0.8946 (tt0) cc_final: 0.8663 (tt0)
REVERT: A  298 GLU cc_start: 0.8931 (tt0) cc_final: 0.8592 (tt0)
REVERT: A  306 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8684 (mm110)
REVERT: A  315 ASP cc_start: 0.9226 (p0) cc_final: 0.8863 (p0)
REVERT: B   16 ASN cc_start: 0.8763 (m-40) cc_final: 0.8138 (m-40)
REVERT: B   19 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8536 (tmm-80)
REVERT: B   46 ARG cc_start: 0.8128 (mpt90) cc_final: 0.7816 (mtm-85)
REVERT: B  214 ARG cc_start: 0.9091 (tpp80) cc_final: 0.8751 (mmt90)
REVERT: B  215 GLU cc_start: 0.8032 (pt0) cc_final: 0.7528 (tm-30)
REVERT: B  217 MET cc_start: 0.9082 (ptp) cc_final: 0.7791 (ptp)
REVERT: B  260 GLU cc_start: 0.8244 (pt0) cc_final: 0.7814 (tt0)
REVERT: G   31 SER cc_start: 0.8029 (t) cc_final: 0.7801 (m)
REVERT: G   42 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8141 (pp20)
REVERT: S   43 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8405 (mtmm)
REVERT: S   82 GLN cc_start: 0.8278 (tp40) cc_final: 0.7760 (tp-100)
REVERT: S   87 ARG cc_start: 0.8734 (pmm-80) cc_final: 0.8456 (pmm-80)
REVERT: S  160 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7438 (mtp85)
REVERT: S  186 GLN cc_start: 0.8538 (mt0) cc_final: 0.8138 (tt0)
REVERT: S  235 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6706 (t80)
REVERT: S  244 LYS cc_start: 0.8866 (tttp) cc_final: 0.8581 (ttpp)
REVERT: R   85 ARG cc_start: 0.8378 (mtm110) cc_final: 0.7639 (mtm180)
REVERT: R  113 ASN cc_start: 0.8613 (m-40) cc_final: 0.8003 (t0)
REVERT: R  157 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8209 (mtpt)
REVERT: R  200 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7581 (mmmm)
REVERT: R  201 THR cc_start: 0.8661 (p) cc_final: 0.8349 (m)
REVERT: R  263 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: R  303 MET cc_start: 0.6674 (tpp) cc_final: 0.6460 (ttp)
  outliers start: 24
  outliers final: 14
  residues processed: 181
  average time/residue: 1.3301
  time to fit residues: 254.7961
Evaluate side-chains
  183 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 SER
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 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  157 LYS
Chi-restraints excluded: chain R residue  278 CYS
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 92 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 107 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
B 259 GLN
** R  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.103623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.071017 restraints weight = 14846.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.94
r_work: 0.2791 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8913  Z= 0.197
  Angle     :  0.633  11.779  12119  Z= 0.320
  Chirality :  0.043   0.229   1372
  Planarity :  0.005   0.057   1529
  Dihedral  :  4.618  37.826   1227
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.09 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1117
  helix:  2.43 (0.26), residues: 392
  sheet: -0.85 (0.29), residues: 274
  loop : -0.83 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  59 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.017   0.002   PHE R 279 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.010   0.001   ARG R  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04014 (  426)
  hydrogen bonds       : angle       4.50825 ( 1230)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       0.13688 (    2)
  covalent geometry    : bond        0.00459 ( 8911)
  covalent geometry    : angle       0.63267 (12117)
  Misc. bond           : bond        0.00112 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8514.56 seconds
wall clock time: 148 minutes 49.27 seconds (8929.27 seconds total)