Starting phenix.real_space_refine
on Sun May 11 13:00:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dtg_47155/05_2025/9dtg_47155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dtg_47155/05_2025/9dtg_47155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dtg_47155/05_2025/9dtg_47155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dtg_47155/05_2025/9dtg_47155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dtg_47155/05_2025/9dtg_47155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dtg_47155/05_2025/9dtg_47155.cif"
  }
  resolution = 3.83
  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=   0.023
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      46      5.16       5
     C    5104      2.51       5
     N    1386      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8069
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4039
          Classifications: {'peptide': 512}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 496}
    Chain: "B"
      Number of atoms: 4030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4030
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 15, 'TRANS': 495}
          Chain breaks: 1
  Time building chain proxies: 5.93, per 1000 atoms: 0.73
  Number of scatterers: 8069
  At special positions: 0
  Unit cell: (74.34, 98.235, 138.945, 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      46     16.00
     O    1533      8.00
     N    1386      7.00
     C    5104      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 147 " - pdb=" SG  CYS A 169 " 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: 2.02
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 19 sheets defined
      24.5% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 67
      removed outlier: 3.723A  pdb=" N   GLN A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 76
    Processing helix  chain 'A' and resid 78 through 83
      removed outlier: 4.077A  pdb=" N   HIS A  82 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASN A  83 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
      removed outlier: 4.074A  pdb=" N   GLN A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR A 104 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 115
      removed outlier: 3.555A  pdb=" N   LEU A 115 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 112 through 115'
    Processing helix  chain 'A' and resid 116 through 125
      removed outlier: 3.643A  pdb=" N   GLU A 120 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER A 122 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP A 123 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 139
      removed outlier: 4.204A  pdb=" N   ARG A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 155
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 3.554A  pdb=" N   THR A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 178
      removed outlier: 3.640A  pdb=" N   LEU A 177 " --> pdb=" O   HIS A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
      removed outlier: 3.934A  pdb=" N   LEU A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   HIS A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 185'
    Processing helix  chain 'A' and resid 187 through 195
      removed outlier: 4.205A  pdb=" N   ASP A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.718A  pdb=" N   ILE A 209 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLU A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 230
      removed outlier: 4.233A  pdb=" N   GLU A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   SER A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.927A  pdb=" N   TRP A 460 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 461 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 461'
    Processing helix  chain 'B' and resid 31 through 39
      removed outlier: 3.688A  pdb=" N   LYS B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LEU B  37 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 67
      removed outlier: 3.572A  pdb=" N   LEU B  63 " --> pdb=" O   HIS B  59 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER B  64 " --> pdb=" O   ARG B  60 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 3.652A  pdb=" N   PHE B  74 " --> pdb=" O   PHE B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 104
      removed outlier: 3.538A  pdb=" N   GLN B  97 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 125
    Processing helix  chain 'B' and resid 129 through 132
    Processing helix  chain 'B' and resid 133 through 139
      removed outlier: 3.656A  pdb=" N   LEU B 138 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 147
    Processing helix  chain 'B' and resid 148 through 155
    Processing helix  chain 'B' and resid 159 through 164
    Processing helix  chain 'B' and resid 167 through 172
      removed outlier: 4.159A  pdb=" N   THR B 172 " --> pdb=" O   HIS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 180
      removed outlier: 4.329A  pdb=" N   ASN B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   THR B 180 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 185
      removed outlier: 3.965A  pdb=" N   LEU B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 185'
    Processing helix  chain 'B' and resid 187 through 196
      removed outlier: 3.522A  pdb=" N   THR B 192 " --> pdb=" O   HIS B 188 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASP B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
      removed outlier: 3.746A  pdb=" N   ALA B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ILE B 209 " --> pdb=" O   PRO B 205 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   TRP B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 3.880A  pdb=" N   ALA B 222 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE B 223 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 219 through 223'
    Processing helix  chain 'B' and resid 326 through 330
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
    Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200
      removed outlier: 6.291A  pdb=" N   VAL A 199 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 271
      removed outlier: 5.241A  pdb=" N   SER A 256 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   GLN A 270 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   ALA A 254 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 243 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.892A  pdb=" N   VAL A 290 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP A 286 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.892A  pdb=" N   VAL A 290 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY A 291 " --> pdb=" O   ARG A 297 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326
      removed outlier: 3.555A  pdb=" N   VAL A 324 " --> pdb=" O   TYR A 333 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL A 326 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA A 331 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 351 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374
    Processing sheet with id=AA9, first strand: chain 'A' and resid 386 through 388
    Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 428
    Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 472
      removed outlier: 3.744A  pdb=" N   CYS A 472 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 49
      removed outlier: 3.536A  pdb=" N   VAL B  47 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 200
      removed outlier: 5.666A  pdb=" N   VAL B 199 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 270 through 272
      removed outlier: 4.098A  pdb=" N   ASN B 271 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 257 " --> pdb=" O   ILE B 240 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B 515 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 277 through 283
      removed outlier: 3.579A  pdb=" N   GLY B 291 " --> pdb=" O   ARG B 297 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG B 297 " --> pdb=" O   GLY B 291 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 322 through 323
    Processing sheet with id=AB8, first strand: chain 'B' and resid 372 through 376
      removed outlier: 3.887A  pdb=" N   CYS B 402 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   HIS B 411 " --> pdb=" O   CYS B 402 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 424 through 428
      removed outlier: 3.607A  pdb=" N   ALA B 426 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE B 433 " --> pdb=" O   ALA B 426 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL B 432 " --> pdb=" O   TYR B 444 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 467 through 472
      removed outlier: 3.643A  pdb=" N   CYS B 472 " --> pdb=" O   SER B 475 " (cutoff:3.500A)

    164 hydrogen bonds defined for protein.
    414 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: 2.13

  Time building geometry restraints manager: 2.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2441
        1.33 -     1.45: 1225
        1.45 -     1.57: 4517
        1.57 -     1.69: 1
        1.69 -     1.81: 60
  Bond restraints: 8244
  Sorted by residual:
  bond pdb=" N   SER A 325 "
       pdb=" CA  SER A 325 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.26e-02 6.30e+03 1.06e+01
  bond pdb=" N   VAL A 326 "
       pdb=" CA  VAL A 326 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.23e-02 6.61e+03 9.96e+00
  bond pdb=" N   LYS A 329 "
       pdb=" CA  LYS A 329 "
    ideal  model  delta    sigma   weight residual
    1.462  1.499 -0.037 1.32e-02 5.74e+03 7.76e+00
  bond pdb=" N   LYS B 329 "
       pdb=" CA  LYS B 329 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.19e-02 7.06e+03 6.80e+00
  bond pdb=" CA  SER A 325 "
       pdb=" CB  SER A 325 "
    ideal  model  delta    sigma   weight residual
    1.534  1.489  0.044 1.72e-02 3.38e+03 6.66e+00
  ... (remaining 8239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11013
        2.17 -     4.33: 151
        4.33 -     6.50: 20
        6.50 -     8.66: 5
        8.66 -    10.83: 3
  Bond angle restraints: 11192
  Sorted by residual:
  angle pdb=" N   ASP B  12 "
        pdb=" CA  ASP B  12 "
        pdb=" C   ASP B  12 "
      ideal   model   delta    sigma   weight residual
     112.54  104.48    8.06 1.51e+00 4.39e-01 2.85e+01
  angle pdb=" N   GLY A 328 "
        pdb=" CA  GLY A 328 "
        pdb=" C   GLY A 328 "
      ideal   model   delta    sigma   weight residual
     115.73  107.56    8.17 1.59e+00 3.96e-01 2.64e+01
  angle pdb=" C   LYS A 429 "
        pdb=" CA  LYS A 429 "
        pdb=" CB  LYS A 429 "
      ideal   model   delta    sigma   weight residual
     116.54  110.68    5.86 1.15e+00 7.56e-01 2.59e+01
  angle pdb=" N   MET A  11 "
        pdb=" CA  MET A  11 "
        pdb=" C   MET A  11 "
      ideal   model   delta    sigma   weight residual
     113.23  107.71    5.52 1.24e+00 6.50e-01 1.98e+01
  angle pdb=" C   ALA A   9 "
        pdb=" N   SER A  10 "
        pdb=" CA  SER A  10 "
      ideal   model   delta    sigma   weight residual
     121.54  129.74   -8.20 1.91e+00 2.74e-01 1.84e+01
  ... (remaining 11187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4391
       17.97 -    35.94: 414
       35.94 -    53.91: 90
       53.91 -    71.88: 12
       71.88 -    89.86: 2
  Dihedral angle restraints: 4909
    sinusoidal: 1919
      harmonic: 2990
  Sorted by residual:
  dihedral pdb=" CA  TYR B 104 "
           pdb=" C   TYR B 104 "
           pdb=" N   HIS B 105 "
           pdb=" CA  HIS B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.64  -26.36     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  MET B  11 "
           pdb=" C   MET B  11 "
           pdb=" N   ASP B  12 "
           pdb=" CA  ASP B  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  VAL B  17 "
           pdb=" C   VAL B  17 "
           pdb=" N   ASN B  18 "
           pdb=" CA  ASN B  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 4906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1117
       0.063 -    0.126: 136
       0.126 -    0.188: 12
       0.188 -    0.251: 1
       0.251 -    0.314: 1
  Chirality restraints: 1267
  Sorted by residual:
  chirality pdb=" CB  VAL A 326 "
            pdb=" CA  VAL A 326 "
            pdb=" CG1 VAL A 326 "
            pdb=" CG2 VAL A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CA  VAL B 326 "
            pdb=" N   VAL B 326 "
            pdb=" C   VAL B 326 "
            pdb=" CB  VAL B 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  VAL A 326 "
            pdb=" N   VAL A 326 "
            pdb=" C   VAL A 326 "
            pdb=" CB  VAL A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 1264 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 294 "   -0.033 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 295 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 295 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 295 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  20 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.91e+00
        pdb=" C   THR B  20 "    0.024 2.00e-02 2.50e+03
        pdb=" O   THR B  20 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE B  21 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 500 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   VAL A 500 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL A 500 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   THR A 501 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 565
        2.74 -     3.28: 7605
        3.28 -     3.82: 11608
        3.82 -     4.36: 13755
        4.36 -     4.90: 23817
  Nonbonded interactions: 57350
  Sorted by model distance:
  nonbonded pdb=" O   SER B 196 "
            pdb=" OG  SER B 196 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG1 THR A 339 "
            pdb=" OG1 THR A 343 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   THR A 490 "
            pdb=" OG1 THR A 490 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER B 247 "
            pdb=" OG1 THR B 511 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASN A 271 "
            pdb=" NE1 TRP A 308 "
     model   vdw
     2.282 3.120
  ... (remaining 57345 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 216 or resid 218 through 518))
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.560
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     22.310
  Find NCS groups from input model:        0.290
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
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   0.046   8245  Z= 0.166
  Angle     :  0.651  10.829  11194  Z= 0.368
  Chirality :  0.044   0.314   1267
  Planarity :  0.003   0.048   1438
  Dihedral  : 14.386  89.856   2972
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.24 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 22.16 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.94 (0.24), residues: 1017
  helix: -3.59 (0.26), residues: 224
  sheet: -2.59 (0.35), residues: 218
  loop : -2.20 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.008   0.001   PHE B  16 
 TYR   0.016   0.001   TYR A 241 
 ARG   0.005   0.000   ARG B 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.33424 (  163)
  hydrogen bonds       : angle      11.40189 (  414)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.62975 (    2)
  covalent geometry    : bond        0.00291 ( 8244)
  covalent geometry    : angle       0.65075 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.811 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 83
  average time/residue: 0.2114
  time to fit residues: 24.1110
Evaluate side-chains
  78 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue  105 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 77 optimal weight:   20.0000
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.174115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.160252 restraints weight = 8543.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.158538 restraints weight = 21299.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.143960 restraints weight = 21504.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8245  Z= 0.170
  Angle     :  0.584   8.263  11194  Z= 0.308
  Chirality :  0.045   0.148   1267
  Planarity :  0.004   0.030   1438
  Dihedral  :  4.934  43.206   1112
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.13 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 19.01 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -4.12 (0.23), residues: 1017
  helix: -3.28 (0.25), residues: 244
  sheet: -2.69 (0.34), residues: 214
  loop : -2.49 (0.23), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 299 
 HIS   0.004   0.001   HIS A 258 
 PHE   0.014   0.002   PHE A  96 
 TYR   0.019   0.002   TYR B  19 
 ARG   0.003   0.000   ARG B 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04135 (  163)
  hydrogen bonds       : angle       6.56268 (  414)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.42543 (    2)
  covalent geometry    : bond        0.00410 ( 8244)
  covalent geometry    : angle       0.58372 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 93
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8506 (tppt) cc_final: 0.7910 (ttmt)
REVERT: A  300 LYS cc_start: 0.8371 (tttt) cc_final: 0.8169 (tttm)
  outliers start: 45
  outliers final: 23
  residues processed: 128
  average time/residue: 0.1983
  time to fit residues: 35.5089
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 80 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 489 ASN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.172136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.155232 restraints weight = 8689.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.152607 restraints weight = 16474.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.152018 restraints weight = 21400.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8245  Z= 0.165
  Angle     :  0.570   9.160  11194  Z= 0.299
  Chirality :  0.045   0.158   1267
  Planarity :  0.004   0.031   1438
  Dihedral  :  4.945  49.824   1109
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.42 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 19.12 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -4.03 (0.23), residues: 1017
  helix: -3.12 (0.26), residues: 245
  sheet: -2.61 (0.35), residues: 209
  loop : -2.50 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.012   0.001   PHE A  96 
 TYR   0.018   0.002   TYR B  19 
 ARG   0.003   0.000   ARG B 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  163)
  hydrogen bonds       : angle       5.88762 (  414)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.31547 (    2)
  covalent geometry    : bond        0.00400 ( 8244)
  covalent geometry    : angle       0.56987 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 84
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8562 (tppt) cc_final: 0.8040 (ttmt)
  outliers start: 41
  outliers final: 25
  residues processed: 115
  average time/residue: 0.1779
  time to fit residues: 28.7949
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  298 MET
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0870
   chunk 14 optimal weight:    0.5980
   chunk 80 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.172919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.155687 restraints weight = 8616.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 94)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.142035 restraints weight = 15003.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.139456 restraints weight = 17233.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8245  Z= 0.131
  Angle     :  0.530   8.366  11194  Z= 0.280
  Chirality :  0.043   0.154   1267
  Planarity :  0.003   0.029   1438
  Dihedral  :  4.867  55.612   1109
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.13 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 20.02 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.95 (0.23), residues: 1017
  helix: -2.97 (0.27), residues: 240
  sheet: -2.65 (0.34), residues: 209
  loop : -2.47 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 460 
 HIS   0.002   0.001   HIS A 258 
 PHE   0.011   0.001   PHE B  96 
 TYR   0.015   0.002   TYR B 119 
 ARG   0.002   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03130 (  163)
  hydrogen bonds       : angle       5.47638 (  414)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.37123 (    2)
  covalent geometry    : bond        0.00316 ( 8244)
  covalent geometry    : angle       0.52973 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 83
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8605 (tppt) cc_final: 0.8064 (ttmt)
REVERT: A  299 TRP cc_start: 0.9026 (m-90) cc_final: 0.8782 (m-10)
REVERT: A  300 LYS cc_start: 0.8410 (tttt) cc_final: 0.7997 (tttt)
REVERT: B   19 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6333 (m-80)
REVERT: B  344 LEU cc_start: 0.1101 (OUTLIER) cc_final: 0.0848 (mt)
  outliers start: 44
  outliers final: 28
  residues processed: 118
  average time/residue: 0.1863
  time to fit residues: 30.8715
Evaluate side-chains
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.1980
   chunk 99 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 56 optimal weight:    0.3980
   chunk 73 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 57 optimal weight:    0.1980
   chunk 83 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 GLN
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.174046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160641 restraints weight = 8536.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.157394 restraints weight = 12631.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.156128 restraints weight = 16745.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8245  Z= 0.109
  Angle     :  0.503   8.174  11194  Z= 0.266
  Chirality :  0.043   0.159   1267
  Planarity :  0.003   0.031   1438
  Dihedral  :  4.773  59.603   1109
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.32 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 21.15 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.85 (0.23), residues: 1017
  helix: -2.82 (0.28), residues: 239
  sheet: -2.60 (0.34), residues: 209
  loop : -2.42 (0.23), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A 428 
 PHE   0.009   0.001   PHE B  96 
 TYR   0.014   0.001   TYR B 119 
 ARG   0.003   0.000   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02838 (  163)
  hydrogen bonds       : angle       5.21739 (  414)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.36840 (    2)
  covalent geometry    : bond        0.00258 ( 8244)
  covalent geometry    : angle       0.50265 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 80
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8505 (tppt) cc_final: 0.8075 (ttmt)
REVERT: A  195 ILE cc_start: 0.8805 (mm) cc_final: 0.8596 (mt)
REVERT: A  299 TRP cc_start: 0.8917 (m-90) cc_final: 0.8712 (m-10)
REVERT: B   19 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6359 (m-80)
REVERT: B  114 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8166 (pp20)
REVERT: B  344 LEU cc_start: 0.1746 (OUTLIER) cc_final: 0.1363 (mt)
  outliers start: 40
  outliers final: 28
  residues processed: 113
  average time/residue: 0.1549
  time to fit residues: 25.6287
Evaluate side-chains
  105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0670
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0870
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.175186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.161893 restraints weight = 8509.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.159811 restraints weight = 12332.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.158146 restraints weight = 16487.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8245  Z= 0.107
  Angle     :  0.512  10.675  11194  Z= 0.264
  Chirality :  0.043   0.163   1267
  Planarity :  0.003   0.027   1438
  Dihedral  :  4.652  56.669   1109
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.42 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 20.36 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.73 (0.23), residues: 1017
  helix: -2.66 (0.29), residues: 239
  sheet: -2.55 (0.34), residues: 204
  loop : -2.37 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A 321 
 PHE   0.010   0.001   PHE B  96 
 TYR   0.014   0.001   TYR B 119 
 ARG   0.002   0.000   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02724 (  163)
  hydrogen bonds       : angle       5.00036 (  414)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       0.34384 (    2)
  covalent geometry    : bond        0.00253 ( 8244)
  covalent geometry    : angle       0.51231 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 79
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8527 (tppt) cc_final: 0.8119 (ttmt)
REVERT: B   19 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6317 (m-80)
REVERT: B   26 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7107 (m170)
REVERT: B  114 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8154 (pp20)
REVERT: B  344 LEU cc_start: 0.2006 (OUTLIER) cc_final: 0.1467 (mt)
  outliers start: 46
  outliers final: 27
  residues processed: 119
  average time/residue: 0.1692
  time to fit residues: 29.3770
Evaluate side-chains
  106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 93 optimal weight:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 97 optimal weight:    0.1980
   chunk 72 optimal weight:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 85 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.173107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.155876 restraints weight = 8555.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.150574 restraints weight = 15194.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.149234 restraints weight = 21144.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8245  Z= 0.138
  Angle     :  0.542   9.059  11194  Z= 0.280
  Chirality :  0.044   0.179   1267
  Planarity :  0.003   0.028   1438
  Dihedral  :  4.821  55.036   1109
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.60 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 20.81 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.72 (0.24), residues: 1017
  helix: -2.67 (0.29), residues: 239
  sheet: -2.58 (0.34), residues: 209
  loop : -2.34 (0.23), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 275 
 PHE   0.012   0.001   PHE B  16 
 TYR   0.016   0.002   TYR B 119 
 ARG   0.001   0.000   ARG B  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02950 (  163)
  hydrogen bonds       : angle       5.07250 (  414)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.30415 (    2)
  covalent geometry    : bond        0.00335 ( 8244)
  covalent geometry    : angle       0.54239 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 81
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8565 (tppt) cc_final: 0.8143 (ttmt)
REVERT: A  258 HIS cc_start: 0.8351 (t-90) cc_final: 0.7950 (t70)
REVERT: B   19 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6509 (m-80)
REVERT: B  114 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8168 (pp20)
REVERT: B  318 ARG cc_start: 0.6342 (mtt180) cc_final: 0.6120 (mtt180)
REVERT: B  344 LEU cc_start: 0.2235 (OUTLIER) cc_final: 0.1809 (mt)
  outliers start: 43
  outliers final: 31
  residues processed: 117
  average time/residue: 0.1646
  time to fit residues: 27.9307
Evaluate side-chains
  113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 79
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.171399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.157477 restraints weight = 8676.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.152147 restraints weight = 14154.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.150562 restraints weight = 20780.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8245  Z= 0.163
  Angle     :  0.561   8.687  11194  Z= 0.293
  Chirality :  0.045   0.198   1267
  Planarity :  0.003   0.031   1438
  Dihedral  :  4.985  52.814   1109
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.60 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.37 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.77 (0.23), residues: 1017
  helix: -2.74 (0.29), residues: 239
  sheet: -2.66 (0.33), residues: 209
  loop : -2.34 (0.23), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.014   0.001   PHE B  16 
 TYR   0.018   0.002   TYR B  19 
 ARG   0.002   0.000   ARG A 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03068 (  163)
  hydrogen bonds       : angle       5.20514 (  414)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.31005 (    2)
  covalent geometry    : bond        0.00397 ( 8244)
  covalent geometry    : angle       0.56143 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 86
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8582 (tppt) cc_final: 0.8148 (ttmt)
REVERT: A  258 HIS cc_start: 0.8303 (t-90) cc_final: 0.7913 (t70)
REVERT: B   19 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6717 (m-80)
REVERT: B  114 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (pp20)
REVERT: B  318 ARG cc_start: 0.6401 (mtt180) cc_final: 0.6126 (mtt180)
REVERT: B  344 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.2249 (mt)
  outliers start: 44
  outliers final: 30
  residues processed: 121
  average time/residue: 0.1815
  time to fit residues: 31.4514
Evaluate side-chains
  116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 83
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 72 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   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  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.171632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.157784 restraints weight = 8797.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.154171 restraints weight = 13531.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.152453 restraints weight = 18812.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8245  Z= 0.156
  Angle     :  0.554   7.930  11194  Z= 0.292
  Chirality :  0.044   0.202   1267
  Planarity :  0.003   0.031   1438
  Dihedral  :  4.957  51.973   1109
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.50 %
    Favored  : 88.40 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 21.37 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.82 (0.23), residues: 1017
  helix: -2.75 (0.28), residues: 239
  sheet: -2.71 (0.32), residues: 219
  loop : -2.34 (0.24), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.013   0.001   PHE B  96 
 TYR   0.018   0.002   TYR B  19 
 ARG   0.002   0.000   ARG A 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03043 (  163)
  hydrogen bonds       : angle       5.18573 (  414)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       0.34069 (    2)
  covalent geometry    : bond        0.00380 ( 8244)
  covalent geometry    : angle       0.55399 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 84
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8590 (tppt) cc_final: 0.8172 (ttmt)
REVERT: A  258 HIS cc_start: 0.8310 (t-90) cc_final: 0.7915 (t70)
REVERT: B   19 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6667 (m-80)
REVERT: B  114 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8132 (pp20)
REVERT: B  318 ARG cc_start: 0.6201 (mtt180) cc_final: 0.5987 (mtt180)
REVERT: B  344 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.2423 (mt)
  outliers start: 45
  outliers final: 34
  residues processed: 120
  average time/residue: 0.1778
  time to fit residues: 30.5661
Evaluate side-chains
  119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  452 THR
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0670
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0870
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.173823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.159496 restraints weight = 8587.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.155363 restraints weight = 14839.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.153333 restraints weight = 20170.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8245  Z= 0.120
  Angle     :  0.546  11.630  11194  Z= 0.283
  Chirality :  0.044   0.200   1267
  Planarity :  0.003   0.029   1438
  Dihedral  :  4.771  50.002   1109
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.82 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.82 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.76 (0.23), residues: 1017
  helix: -2.65 (0.29), residues: 240
  sheet: -2.69 (0.32), residues: 220
  loop : -2.32 (0.23), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 299 
 HIS   0.002   0.000   HIS A 258 
 PHE   0.011   0.001   PHE B  96 
 TYR   0.016   0.002   TYR B 119 
 ARG   0.001   0.000   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02747 (  163)
  hydrogen bonds       : angle       5.03694 (  414)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.38281 (    2)
  covalent geometry    : bond        0.00285 ( 8244)
  covalent geometry    : angle       0.54594 (11192)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 81
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8582 (tppt) cc_final: 0.8171 (ttmt)
REVERT: A  258 HIS cc_start: 0.8239 (t-90) cc_final: 0.7890 (t70)
REVERT: B   19 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6530 (m-80)
REVERT: B  114 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8126 (pp20)
REVERT: B  344 LEU cc_start: 0.2629 (OUTLIER) cc_final: 0.2311 (mt)
  outliers start: 38
  outliers final: 32
  residues processed: 111
  average time/residue: 0.1924
  time to fit residues: 30.0975
Evaluate side-chains
  115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 80
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  449 ASP
Chi-restraints excluded: chain B residue  452 THR
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0010
   chunk 79 optimal weight:    0.0970
   chunk 76 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.174680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.161901 restraints weight = 8617.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.158896 restraints weight = 18909.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157980 restraints weight = 22789.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8245  Z= 0.109
  Angle     :  0.543  12.923  11194  Z= 0.278
  Chirality :  0.043   0.200   1267
  Planarity :  0.003   0.030   1438
  Dihedral  :  4.651  48.467   1109
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.42 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 22.05 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -3.60 (0.23), residues: 1017
  helix: -2.56 (0.29), residues: 240
  sheet: -2.57 (0.34), residues: 201
  loop : -2.25 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 299 
 HIS   0.002   0.000   HIS A 321 
 PHE   0.009   0.001   PHE B  96 
 TYR   0.014   0.001   TYR B 119 
 ARG   0.003   0.000   ARG B 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02634 (  163)
  hydrogen bonds       : angle       4.92300 (  414)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.40141 (    2)
  covalent geometry    : bond        0.00256 ( 8244)
  covalent geometry    : angle       0.54275 (11192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2617.97 seconds
wall clock time: 46 minutes 44.74 seconds (2804.74 seconds total)