Starting phenix.real_space_refine
on Wed Jan 15 11:38:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jkq_61567/01_2025/9jkq_61567.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jkq_61567/01_2025/9jkq_61567.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jkq_61567/01_2025/9jkq_61567.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jkq_61567/01_2025/9jkq_61567.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jkq_61567/01_2025/9jkq_61567.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jkq_61567/01_2025/9jkq_61567.cif"
  }
  resolution = 2.66
  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=  -0.002 sd=   0.078
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      63      5.16       5
     C    5336      2.51       5
     N    1446      2.21       5
     O    1541      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8386
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1947
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "C"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 442
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2407
          Classifications: {'peptide': 296}
          Link IDs: {'PTRANS': 11, 'TRANS': 284}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'B40': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.07, per 1000 atoms: 0.60
  Number of scatterers: 8386
  At special positions: 0
  Unit cell: (79.143, 102.12, 134.458, 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      63     16.00
     O    1541      8.00
     N    1446      7.00
     C    5336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 973.9 milliseconds
  

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  B40 R 401 "
  Number of C-beta restraints generated:  1986

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      41.8% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.570A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 60
      removed outlier: 3.585A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.567A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.708A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 3.838A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 37
    Processing helix  chain 'B' and resid 40 through 46
      removed outlier: 3.765A  pdb=" N   ILE B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 3.665A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.566A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.550A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.959A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 19 through 51
      removed outlier: 3.620A  pdb=" N   ASN R  41 " --> pdb=" O   THR R  37 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   PHE R  51 " --> pdb=" O   SER R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 76
      removed outlier: 3.531A  pdb=" N   LEU R  61 " --> pdb=" O   PRO R  57 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL R  76 " --> pdb=" O   LEU R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 87
    Processing helix  chain 'R' and resid 94 through 127
      removed outlier: 5.947A  pdb=" N   THR R 100 " --> pdb=" O   CYS R  96 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER R 101 " --> pdb=" O   LYS R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 160
      Proline residue:  R 151  - end of helix
      removed outlier: 3.629A  pdb=" N   PHE R 160 " --> pdb=" O   PHE R 156 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 169 through 179
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 230
      removed outlier: 4.007A  pdb=" N   ARG R 212 " --> pdb=" O   CYS R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 274
      removed outlier: 3.707A  pdb=" N   PHE R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      removed outlier: 3.885A  pdb=" N   MET R 273 " --> pdb=" O   ILE R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 278
      removed outlier: 3.620A  pdb=" N   HIS R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 275 through 278'
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.939A  pdb=" N   ASN R 296 " --> pdb=" O   PHE R 292 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   THR R 298 " --> pdb=" O   TYR R 294 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 322
      removed outlier: 3.613A  pdb=" N   ARG R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.269A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.770A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.723A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62
      removed outlier: 3.648A  pdb=" N   ARG B  57 " --> pdb=" O   ASN B 351 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE B 349 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   THR B  61 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU B 347 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   CYS B 328 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74
      removed outlier: 4.059A  pdb=" N   ALA B  71 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LYS B  89 " --> pdb=" O   SER B  85 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ASP B  94 " --> pdb=" O   LYS B 100 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   LYS B 100 " --> pdb=" O   ASP B  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116
      removed outlier: 6.866A  pdb=" N   GLY B 126 " --> pdb=" O   MET B 112 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   CYS B 114 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ALA B 124 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 122 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   TYR B 122 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLY B 127 " --> pdb=" O   ILE B 131 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   ILE B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   ASN B 136 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL B 146 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 162
      removed outlier: 3.666A  pdb=" N   CYS B 159 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE B 168 " --> pdb=" O   TRP B 180 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR B 189 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ASP B 181 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN B 187 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203
      removed outlier: 6.859A  pdb=" N   GLY B 213 " --> pdb=" O   MET B 199 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   LEU B 201 " --> pdb=" O   VAL B 211 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 211 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   LEU B 209 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN B 231 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ASP B 223 " --> pdb=" O   CYS B 229 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   CYS B 229 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245
      removed outlier: 6.504A  pdb=" N   GLY B 255 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ILE B 243 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA B 253 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   PHE B 245 " --> pdb=" O   ALA B 251 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   ALA B 251 " --> pdb=" O   PHE B 245 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   MET B 273 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ASP B 265 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   GLU B 271 " --> pdb=" O   ASP B 265 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289
      removed outlier: 3.513A  pdb=" N   SER B 286 " --> pdb=" O   GLY B 299 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   CYS B 305 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   VAL B 318 " --> pdb=" O   CYS B 305 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL B 307 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.558A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.490A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1191 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: 2.40

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2713
        1.34 -     1.46: 1934
        1.46 -     1.58: 3829
        1.58 -     1.70: 0
        1.70 -     1.81: 92
  Bond restraints: 8568
  Sorted by residual:
  bond pdb=" CB  B40 R 401 "
       pdb=" CG  B40 R 401 "
    ideal  model  delta    sigma   weight residual
    1.501  1.521 -0.020 2.00e-02 2.50e+03 1.00e+00
  bond pdb=" SD  MET R  30 "
       pdb=" CE  MET R  30 "
    ideal  model  delta    sigma   weight residual
    1.791  1.767  0.024 2.50e-02 1.60e+03 9.35e-01
  bond pdb=" CA  THR B 207 "
       pdb=" C   THR B 207 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.57e-02 4.06e+03 7.84e-01
  bond pdb=" CG1 ILE A 348 "
       pdb=" CD1 ILE A 348 "
    ideal  model  delta    sigma   weight residual
    1.513  1.484  0.029 3.90e-02 6.57e+02 5.60e-01
  bond pdb=" CG1 ILE R 290 "
       pdb=" CD1 ILE R 290 "
    ideal  model  delta    sigma   weight residual
    1.513  1.484  0.029 3.90e-02 6.57e+02 5.41e-01
  ... (remaining 8563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 11307
        1.43 -     2.86: 240
        2.86 -     4.29: 30
        4.29 -     5.72: 13
        5.72 -     7.15: 1
  Bond angle restraints: 11591
  Sorted by residual:
  angle pdb=" CA  TYR R  90 "
        pdb=" CB  TYR R  90 "
        pdb=" CG  TYR R  90 "
      ideal   model   delta    sigma   weight residual
     113.90  118.62   -4.72 1.80e+00 3.09e-01 6.89e+00
  angle pdb=" N   CYS R  96 "
        pdb=" CA  CYS R  96 "
        pdb=" C   CYS R  96 "
      ideal   model   delta    sigma   weight residual
     113.20  109.87    3.33 1.36e+00 5.41e-01 5.98e+00
  angle pdb=" N   LYS R  97 "
        pdb=" CA  LYS R  97 "
        pdb=" C   LYS R  97 "
      ideal   model   delta    sigma   weight residual
     114.62  111.84    2.78 1.14e+00 7.69e-01 5.94e+00
  angle pdb=" CA  TRP R 291 "
        pdb=" CB  TRP R 291 "
        pdb=" CG  TRP R 291 "
      ideal   model   delta    sigma   weight residual
     113.60  109.05    4.55 1.90e+00 2.77e-01 5.72e+00
  angle pdb=" CA  TRP R  89 "
        pdb=" C   TRP R  89 "
        pdb=" N   TYR R  90 "
      ideal   model   delta    sigma   weight residual
     114.17  117.22   -3.05 1.45e+00 4.76e-01 4.42e+00
  ... (remaining 11586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4659
       17.79 -    35.57: 363
       35.57 -    53.36: 58
       53.36 -    71.15: 7
       71.15 -    88.93: 10
  Dihedral angle restraints: 5097
    sinusoidal: 2024
      harmonic: 3073
  Sorted by residual:
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 182 "
           pdb=" CB  CYS R 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.91  -75.91     1      1.00e+01 1.00e-02 7.26e+01
  dihedral pdb=" CA  CYS R  96 "
           pdb=" C   CYS R  96 "
           pdb=" N   LYS R  97 "
           pdb=" CA  LYS R  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.24   24.76     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  TRP B  93 "
           pdb=" C   TRP B  93 "
           pdb=" N   ASP B  94 "
           pdb=" CA  ASP B  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 5094 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 867
       0.038 -    0.076: 313
       0.076 -    0.114: 91
       0.114 -    0.152: 15
       0.152 -    0.191: 1
  Chirality restraints: 1287
  Sorted by residual:
  chirality pdb=" CA  B40 R 401 "
            pdb=" N   B40 R 401 "
            pdb=" C   B40 R 401 "
            pdb=" CB  B40 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.61    0.19 2.00e-01 2.50e+01 9.08e-01
  chirality pdb=" CA  MET R  77 "
            pdb=" N   MET R  77 "
            pdb=" C   MET R  77 "
            pdb=" CB  MET R  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  VAL N  37 "
            pdb=" N   VAL N  37 "
            pdb=" C   VAL N  37 "
            pdb=" CB  VAL N  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.94e-01
  ... (remaining 1284 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 246 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.28e+00
        pdb=" N   PRO B 247 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  54 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO C  55 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  56 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO R  57 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO R  57 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R  57 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 86
        2.66 -     3.22: 7499
        3.22 -     3.78: 12627
        3.78 -     4.34: 17986
        4.34 -     4.90: 29772
  Nonbonded interactions: 67970
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 256 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" O   ARG N  98 "
            pdb=" OH  TYR N 115 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OG  SER B 292 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ASP A 368 "
            pdb=" OG1 THR A 369 "
     model   vdw
     2.275 3.040
  ... (remaining 67965 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.860
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.910
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:12.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
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      :  0.003   0.029   8568  Z= 0.175
  Angle     :  0.529   7.149  11591  Z= 0.289
  Chirality :  0.042   0.191   1287
  Planarity :  0.004   0.057   1472
  Dihedral  : 13.250  88.932   3105
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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:  0.84 (0.26), residues: 1039
  helix:  1.81 (0.26), residues: 421
  sheet:  0.61 (0.38), residues: 204
  loop : -0.77 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 291 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 162 
 TYR   0.012   0.001   TYR R 172 
 ARG   0.003   0.000   ARG N  67 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.5059 (mtt) cc_final: 0.4565 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 1.2605
  time to fit residues: 187.5049
Evaluate side-chains
  117 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.3980
   chunk 77 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
N   3 GLN
N  31 ASN
N  77 ASN
R 228 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.178697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.134508 restraints weight = 8696.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.87
r_work: 0.3343 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8568  Z= 0.174
  Angle     :  0.530   6.331  11591  Z= 0.293
  Chirality :  0.042   0.143   1287
  Planarity :  0.004   0.057   1472
  Dihedral  :  4.358  22.930   1154
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  8.11 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.97 (0.26), residues: 1039
  helix:  1.89 (0.25), residues: 425
  sheet:  0.77 (0.37), residues: 205
  loop : -0.77 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  93 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 162 
 TYR   0.023   0.001   TYR R  90 
 ARG   0.005   0.000   ARG A  38 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.881 
Fit side-chains
REVERT: A   60 MET cc_start: 0.5146 (mtt) cc_final: 0.4448 (ptp)
REVERT: A  208 PHE cc_start: 0.7460 (m-10) cc_final: 0.7199 (m-10)
REVERT: A  263 THR cc_start: 0.6143 (m) cc_final: 0.5930 (m)
REVERT: N   19 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7091 (ttt180)
  outliers start: 16
  outliers final: 6
  residues processed: 123
  average time/residue: 1.2917
  time to fit residues: 169.0662
Evaluate side-chains
  116 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   26 LEU
Chi-restraints excluded: chain R residue  197 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   chunk 50 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 264 ASN
A 292 ASN
B 186 GLN
N   3 GLN
N  31 ASN
N  77 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.178707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.134404 restraints weight = 8801.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.89
r_work: 0.3340 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8568  Z= 0.170
  Angle     :  0.511   5.721  11591  Z= 0.282
  Chirality :  0.042   0.143   1287
  Planarity :  0.004   0.058   1472
  Dihedral  :  4.307  22.526   1154
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.97 %
    Favored  : 87.84 %
  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:  1.06 (0.26), residues: 1039
  helix:  1.99 (0.26), residues: 425
  sheet:  0.91 (0.37), residues: 204
  loop : -0.79 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  93 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 162 
 TYR   0.036   0.002   TYR R  90 
 ARG   0.006   0.000   ARG A  38 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A   60 MET cc_start: 0.5120 (mtt) cc_final: 0.4423 (ptp)
REVERT: A  209 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7371 (tm-30)
REVERT: A  263 THR cc_start: 0.6179 (m) cc_final: 0.5941 (m)
REVERT: A  364 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7563 (p)
REVERT: B   54 ILE cc_start: 0.8360 (mm) cc_final: 0.8154 (mp)
REVERT: B  228 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7729 (pp-130)
REVERT: B  347 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8472 (mt)
  outliers start: 20
  outliers final: 11
  residues processed: 128
  average time/residue: 1.2146
  time to fit residues: 165.8504
Evaluate side-chains
  128 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   26 LEU
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue  197 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
B 270 GLN
N   3 GLN
N  31 ASN
N  77 ASN
R 296 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.176853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.132639 restraints weight = 8716.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.91
r_work: 0.3315 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8568  Z= 0.240
  Angle     :  0.558   6.881  11591  Z= 0.307
  Chirality :  0.044   0.145   1287
  Planarity :  0.004   0.057   1472
  Dihedral  :  4.518  22.372   1154
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.38 %
    Favored  : 85.65 %
  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:  1.01 (0.26), residues: 1039
  helix:  1.95 (0.26), residues: 423
  sheet:  0.95 (0.37), residues: 205
  loop : -0.86 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  93 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.019   0.002   PHE B 162 
 TYR   0.022   0.002   TYR R 172 
 ARG   0.003   0.000   ARG A 347 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6569 (pp20) cc_final: 0.6291 (pp20)
REVERT: A   60 MET cc_start: 0.5130 (mtt) cc_final: 0.4296 (ptp)
REVERT: A  209 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7267 (tm-30)
REVERT: A  263 THR cc_start: 0.6185 (m) cc_final: 0.5966 (m)
REVERT: A  364 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7587 (p)
REVERT: B  228 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7939 (ptt)
REVERT: B  336 MET cc_start: 0.8451 (mtp) cc_final: 0.8213 (mtp)
REVERT: B  347 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8433 (mt)
  outliers start: 18
  outliers final: 11
  residues processed: 129
  average time/residue: 1.2904
  time to fit residues: 177.3829
Evaluate side-chains
  132 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   26 LEU
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue  197 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0060
   chunk 92 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0170
   chunk 15 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.5836

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
N   3 GLN
N  31 ASN
N  77 ASN
R 228 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.179425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135269 restraints weight = 8615.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.83
r_work: 0.3349 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8568  Z= 0.156
  Angle     :  0.492   5.317  11591  Z= 0.272
  Chirality :  0.041   0.137   1287
  Planarity :  0.004   0.057   1472
  Dihedral  :  4.231  22.465   1154
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.69 %
    Favored  : 84.23 %
  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:  1.20 (0.26), residues: 1039
  helix:  2.09 (0.26), residues: 425
  sheet:  1.07 (0.37), residues: 204
  loop : -0.76 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  93 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 162 
 TYR   0.029   0.001   TYR R  90 
 ARG   0.003   0.000   ARG R 121 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6558 (pp20) cc_final: 0.6316 (pp20)
REVERT: A   60 MET cc_start: 0.5127 (mtt) cc_final: 0.4305 (ptp)
REVERT: A  364 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7503 (p)
REVERT: A  386 MET cc_start: 0.8055 (mtp) cc_final: 0.7797 (mtm)
REVERT: B  228 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7807 (pp-130)
REVERT: B  347 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8464 (mt)
  outliers start: 19
  outliers final: 10
  residues processed: 126
  average time/residue: 1.2446
  time to fit residues: 166.9763
Evaluate side-chains
  125 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   26 LEU
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue  183 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    0.1980
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B  86 GLN
B 186 GLN
N   3 GLN
N  31 ASN
R 296 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.176474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.123483 restraints weight = 8626.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.03
r_work: 0.3291 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8568  Z= 0.236
  Angle     :  0.552   6.244  11591  Z= 0.302
  Chirality :  0.043   0.144   1287
  Planarity :  0.004   0.056   1472
  Dihedral  :  4.451  22.172   1154
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.46 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.14 (0.26), residues: 1039
  helix:  2.05 (0.26), residues: 423
  sheet:  1.09 (0.37), residues: 205
  loop : -0.83 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  93 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.019   0.002   PHE B 162 
 TYR   0.013   0.002   TYR N  95 
 ARG   0.004   0.000   ARG R 121 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6436 (pp20) cc_final: 0.6153 (pp20)
REVERT: A   60 MET cc_start: 0.5160 (mtt) cc_final: 0.4285 (ptp)
REVERT: A  209 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7118 (tm-30)
REVERT: A  263 THR cc_start: 0.5987 (OUTLIER) cc_final: 0.5754 (m)
REVERT: A  364 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7467 (p)
REVERT: A  386 MET cc_start: 0.8018 (mtp) cc_final: 0.7649 (mtm)
REVERT: B  228 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7646 (pp-130)
REVERT: B  347 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8403 (mt)
  outliers start: 23
  outliers final: 11
  residues processed: 125
  average time/residue: 1.2898
  time to fit residues: 172.6165
Evaluate side-chains
  125 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   26 LEU
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  196 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 25 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B  86 GLN
B 186 GLN
N   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.178274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.134183 restraints weight = 8665.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.89
r_work: 0.3330 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8568  Z= 0.190
  Angle     :  0.522   5.494  11591  Z= 0.287
  Chirality :  0.042   0.142   1287
  Planarity :  0.004   0.057   1472
  Dihedral  :  4.367  22.413   1154
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.46 %
    Favored  : 82.91 %
  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:  1.15 (0.26), residues: 1039
  helix:  2.04 (0.26), residues: 425
  sheet:  1.17 (0.37), residues: 203
  loop : -0.84 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  93 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 222 
 TYR   0.026   0.001   TYR R  90 
 ARG   0.004   0.000   ARG R 121 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6306 (pp20)
REVERT: A   60 MET cc_start: 0.5175 (mtt) cc_final: 0.4208 (ptp)
REVERT: A  263 THR cc_start: 0.6092 (OUTLIER) cc_final: 0.5856 (m)
REVERT: A  364 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7522 (p)
REVERT: A  386 MET cc_start: 0.8077 (mtp) cc_final: 0.7759 (mtm)
REVERT: B  228 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7859 (pp-130)
REVERT: B  347 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8429 (mt)
REVERT: C   46 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8339 (mttp)
REVERT: N   46 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7927 (pp20)
REVERT: R  212 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7725 (ttt-90)
  outliers start: 24
  outliers final: 14
  residues processed: 126
  average time/residue: 1.2403
  time to fit residues: 166.2939
Evaluate side-chains
  131 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 LEU
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  196 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    0.3980
   chunk 64 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 72 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.178516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136003 restraints weight = 9067.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.13
r_work: 0.3339 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8568  Z= 0.196
  Angle     :  0.526   5.455  11591  Z= 0.290
  Chirality :  0.043   0.142   1287
  Planarity :  0.004   0.057   1472
  Dihedral  :  4.368  22.134   1154
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.12 %
    Favored  : 81.93 %
  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:  1.14 (0.26), residues: 1039
  helix:  2.04 (0.26), residues: 425
  sheet:  1.17 (0.37), residues: 203
  loop : -0.86 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  93 
 HIS   0.005   0.001   HIS R  55 
 PHE   0.018   0.002   PHE A 208 
 TYR   0.023   0.001   TYR R  90 
 ARG   0.004   0.000   ARG R 121 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6169 (pp20)
REVERT: A   60 MET cc_start: 0.5017 (mtt) cc_final: 0.4070 (ptp)
REVERT: A  263 THR cc_start: 0.5998 (OUTLIER) cc_final: 0.5785 (m)
REVERT: A  308 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6176 (mp)
REVERT: A  364 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7493 (p)
REVERT: A  386 MET cc_start: 0.7969 (mtp) cc_final: 0.7602 (mtm)
REVERT: B  228 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7733 (pp-130)
REVERT: B  347 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8444 (mt)
REVERT: C   21 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5416 (ttp)
REVERT: C   46 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8311 (mttp)
REVERT: N   46 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7945 (pp20)
REVERT: R  212 ARG cc_start: 0.7890 (ttt-90) cc_final: 0.7660 (ttt-90)
  outliers start: 27
  outliers final: 16
  residues processed: 128
  average time/residue: 1.2630
  time to fit residues: 171.9862
Evaluate side-chains
  139 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   29 LEU
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  196 MET
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  287 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0370
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.9862

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
N   3 GLN
R 228 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.177905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126688 restraints weight = 9086.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.02
r_work: 0.3332 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8568  Z= 0.203
  Angle     :  0.530   5.440  11591  Z= 0.292
  Chirality :  0.043   0.142   1287
  Planarity :  0.004   0.056   1472
  Dihedral  :  4.394  22.316   1154
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.33 %
    Favored  : 81.82 %
  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:  1.12 (0.26), residues: 1039
  helix:  2.02 (0.26), residues: 425
  sheet:  1.16 (0.37), residues: 203
  loop : -0.88 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  93 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.017   0.002   PHE A 222 
 TYR   0.024   0.001   TYR R  90 
 ARG   0.004   0.000   ARG R 121 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6181 (pp20)
REVERT: A   60 MET cc_start: 0.4949 (mtt) cc_final: 0.4035 (ptp)
REVERT: A  209 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7106 (tm-30)
REVERT: A  263 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5767 (m)
REVERT: A  308 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6159 (mp)
REVERT: A  364 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7488 (p)
REVERT: A  386 MET cc_start: 0.7998 (mtp) cc_final: 0.7620 (mtm)
REVERT: B  228 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7739 (pp-130)
REVERT: B  347 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8442 (mt)
REVERT: C   21 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5428 (ttp)
REVERT: C   46 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8318 (mttp)
REVERT: N   46 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (pp20)
REVERT: R  212 ARG cc_start: 0.7921 (ttt-90) cc_final: 0.7695 (ttt-90)
  outliers start: 26
  outliers final: 15
  residues processed: 129
  average time/residue: 1.2785
  time to fit residues: 175.3112
Evaluate side-chains
  137 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   61 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  196 MET
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  287 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.177632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.134069 restraints weight = 8880.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.05
r_work: 0.3344 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8568  Z= 0.217
  Angle     :  0.542   5.808  11591  Z= 0.298
  Chirality :  0.043   0.144   1287
  Planarity :  0.004   0.056   1472
  Dihedral  :  4.441  22.114   1154
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.44 %
    Favored  : 81.82 %
  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:  1.08 (0.26), residues: 1039
  helix:  1.99 (0.26), residues: 424
  sheet:  1.13 (0.37), residues: 203
  loop : -0.90 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  93 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.020   0.002   PHE A 222 
 TYR   0.023   0.002   TYR R  90 
 ARG   0.004   0.000   ARG R 121 

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

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

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2078 Ramachandran restraints generated.
    1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6187 (pp20)
REVERT: A   60 MET cc_start: 0.4833 (mtt) cc_final: 0.3995 (ptp)
REVERT: A  263 THR cc_start: 0.6023 (OUTLIER) cc_final: 0.5817 (m)
REVERT: A  308 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6201 (mp)
REVERT: A  364 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7510 (p)
REVERT: A  386 MET cc_start: 0.7987 (mtp) cc_final: 0.7611 (mtm)
REVERT: B  228 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7738 (pp-130)
REVERT: B  347 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8420 (mt)
REVERT: C   21 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5444 (ttp)
REVERT: C   46 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8317 (mttp)
REVERT: N    5 GLN cc_start: 0.7089 (tp40) cc_final: 0.6845 (mt0)
REVERT: N   46 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7938 (pp20)
REVERT: R  212 ARG cc_start: 0.7911 (ttt-90) cc_final: 0.7683 (ttt-90)
  outliers start: 25
  outliers final: 14
  residues processed: 127
  average time/residue: 1.2066
  time to fit residues: 163.7978
Evaluate side-chains
  132 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   47 SER
Chi-restraints excluded: chain R residue  183 SER
Chi-restraints excluded: chain R residue  196 MET
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  273 MET
Chi-restraints excluded: chain R residue  287 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0770
   chunk 50 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 101 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0070
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 292 ASN
B 186 GLN
N   3 GLN
R 228 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.179398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.136408 restraints weight = 8719.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.97
r_work: 0.3366 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8568  Z= 0.150
  Angle     :  0.491   5.663  11591  Z= 0.271
  Chirality :  0.041   0.139   1287
  Planarity :  0.004   0.057   1472
  Dihedral  :  4.184  22.384   1154
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.43 %
    Favored  : 81.71 %
  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:  1.23 (0.26), residues: 1039
  helix:  2.13 (0.26), residues: 424
  sheet:  1.19 (0.37), residues: 203
  loop : -0.81 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  55 
 PHE   0.017   0.001   PHE A 222 
 TYR   0.012   0.001   TYR R  90 
 ARG   0.003   0.000   ARG R 121 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7245.43 seconds
wall clock time: 128 minutes 24.13 seconds (7704.13 seconds total)