Starting phenix.real_space_refine
on Wed Mar 12 15:43:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dtg_47155/03_2025/9dtg_47155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dtg_47155/03_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_47155/03_2025/9dtg_47155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dtg_47155/03_2025/9dtg_47155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dtg_47155/03_2025/9dtg_47155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dtg_47155/03_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-5624/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: 5.69, per 1000 atoms: 0.71
  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: 2.03
  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: 1.02
  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: 2.21

  Time building geometry restraints manager: 2.13 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:             18.680
  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:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.530
  Find NCS groups from input model:        0.310
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.060
-------------------------------------------------------------------------------
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   8244  Z= 0.199
  Angle     :  0.651  10.829  11192  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 

*********************** 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  : 1.075 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 83
  average time/residue: 0.2568
  time to fit residues: 28.8628
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  : 0.967 
-------------------------------------------------------------------------------
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 = 8543.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.158545 restraints weight = 21279.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.146272 restraints weight = 21458.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
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   8244  Z= 0.271
  Angle     :  0.584   8.263  11192  Z= 0.308
  Chirality :  0.045   0.148   1267
  Planarity :  0.004   0.030   1438
  Dihedral  :  4.934  43.205   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 

*********************** 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  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8476 (tppt) cc_final: 0.7906 (ttmt)
  outliers start: 45
  outliers final: 23
  residues processed: 128
  average time/residue: 0.2025
  time to fit residues: 36.3200
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  : 0.836 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0980
   chunk 80 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.173108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.156622 restraints weight = 8671.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.155589 restraints weight = 15079.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.154610 restraints weight = 16518.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8244  Z= 0.232
  Angle     :  0.549   8.967  11192  Z= 0.288
  Chirality :  0.044   0.151   1267
  Planarity :  0.003   0.029   1438
  Dihedral  :  4.827  49.662   1109
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.52 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.35 %
    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: -3.99 (0.23), residues: 1017
  helix: -3.07 (0.27), residues: 245
  sheet: -2.59 (0.34), residues: 209
  loop : -2.48 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.011   0.001   PHE B  96 
 TYR   0.016   0.002   TYR B 119 
 ARG   0.003   0.000   ARG B 111 

*********************** 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
  123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 84
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8553 (tppt) cc_final: 0.8031 (ttmt)
  outliers start: 39
  outliers final: 22
  residues processed: 113
  average time/residue: 0.1852
  time to fit residues: 29.7161
Evaluate side-chains
  100 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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 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  199 VAL
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:    0.0770
   chunk 101 optimal weight:    0.0970
   chunk 59 optimal weight:    0.0170
   chunk 14 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 54 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.1974

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.177327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.163680 restraints weight = 8499.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.160838 restraints weight = 12737.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.160533 restraints weight = 14968.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8244  Z= 0.128
  Angle     :  0.495   8.153  11192  Z= 0.260
  Chirality :  0.042   0.143   1267
  Planarity :  0.003   0.027   1438
  Dihedral  :  4.547  55.252   1109
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.05 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 19.69 %
    Favored  : 76.04 %
  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: -3.80 (0.23), residues: 1017
  helix: -2.87 (0.27), residues: 246
  sheet: -2.48 (0.35), residues: 204
  loop : -2.38 (0.23), residues: 567

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   0.008   0.001   PHE B 137 
 TYR   0.012   0.001   TYR B 119 
 ARG   0.002   0.000   ARG B  71 

*********************** 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
  117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 79
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8489 (tppt) cc_final: 0.8002 (ttmt)
REVERT: A  195 ILE cc_start: 0.8769 (mm) cc_final: 0.8522 (mt)
REVERT: A  299 TRP cc_start: 0.8923 (m-90) cc_final: 0.8700 (m-10)
REVERT: B   11 MET cc_start: 0.6733 (tpt) cc_final: 0.6388 (tpt)
REVERT: B   12 ASP cc_start: 0.5980 (t70) cc_final: 0.4406 (m-30)
REVERT: B   19 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6321 (m-80)
REVERT: B  344 LEU cc_start: 0.1476 (OUTLIER) cc_final: 0.1207 (mt)
  outliers start: 38
  outliers final: 24
  residues processed: 111
  average time/residue: 0.1748
  time to fit residues: 28.0580
Evaluate side-chains
  99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  255 VAL
Chi-restraints excluded: chain A residue  281 CYS
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   15 TYR
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  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:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0470
   chunk 83 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.172786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.159356 restraints weight = 8579.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.157058 restraints weight = 12715.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.155812 restraints weight = 16451.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8244  Z= 0.228
  Angle     :  0.532   9.345  11192  Z= 0.279
  Chirality :  0.044   0.163   1267
  Planarity :  0.003   0.031   1438
  Dihedral  :  4.785  57.252   1109
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.93 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 20.81 %
    Favored  : 74.80 %
  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: -3.81 (0.23), residues: 1017
  helix: -2.79 (0.28), residues: 242
  sheet: -2.60 (0.34), residues: 209
  loop : -2.39 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 460 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.012   0.001   PHE B  96 
 TYR   0.017   0.002   TYR B 119 
 ARG   0.007   0.000   ARG A 352 

*********************** 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
  115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8587 (tppt) cc_final: 0.8127 (ttmt)
REVERT: A  195 ILE cc_start: 0.8817 (mm) cc_final: 0.8593 (mt)
REVERT: A  299 TRP cc_start: 0.9000 (m-90) cc_final: 0.8775 (m-10)
REVERT: B   19 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6548 (m-80)
REVERT: B  114 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8125 (pp20)
REVERT: B  344 LEU cc_start: 0.1710 (OUTLIER) cc_final: 0.1366 (mt)
  outliers start: 39
  outliers final: 26
  residues processed: 108
  average time/residue: 0.2031
  time to fit residues: 31.6018
Evaluate side-chains
  100 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
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  513 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.174298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.160891 restraints weight = 8558.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.158226 restraints weight = 12996.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.156922 restraints weight = 16162.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8244  Z= 0.192
  Angle     :  0.526  10.364  11192  Z= 0.273
  Chirality :  0.043   0.171   1267
  Planarity :  0.003   0.027   1438
  Dihedral  :  4.752  58.744   1109
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.93 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 20.81 %
    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: -3.76 (0.23), residues: 1017
  helix: -2.70 (0.28), residues: 239
  sheet: -2.61 (0.33), residues: 209
  loop : -2.35 (0.23), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A 258 
 PHE   0.010   0.001   PHE B  96 
 TYR   0.015   0.002   TYR B 119 
 ARG   0.004   0.000   ARG A 352 

*********************** 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
  118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 76
  time to evaluate  : 0.806 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8537 (tppt) cc_final: 0.8117 (ttmt)
REVERT: A  195 ILE cc_start: 0.8815 (mm) cc_final: 0.8609 (mt)
REVERT: B   19 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6395 (m-80)
REVERT: B  114 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8175 (pp20)
REVERT: B  344 LEU cc_start: 0.1946 (OUTLIER) cc_final: 0.1473 (mt)
  outliers start: 42
  outliers final: 28
  residues processed: 112
  average time/residue: 0.1446
  time to fit residues: 24.7338
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  : 0.798 
-------------------------------------------------------------------------------
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  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 157 HIS
** 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 = 0.3843 r_free = 0.3843 target = 0.166911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.151515 restraints weight = 8746.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.134022 restraints weight = 16578.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.133297 restraints weight = 17060.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   8244  Z= 0.466
  Angle     :  0.697   9.058  11192  Z= 0.361
  Chirality :  0.049   0.226   1267
  Planarity :  0.004   0.036   1438
  Dihedral  :  5.670  59.590   1109
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.88 %
    Favored  : 87.02 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 20.36 %
    Favored  : 74.13 %
  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: -3.15 (0.26), residues: 243
  sheet: -2.86 (0.31), residues: 223
  loop : -2.45 (0.24), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 460 
 HIS   0.005   0.001   HIS A 173 
 PHE   0.018   0.002   PHE B  96 
 TYR   0.034   0.003   TYR B  19 
 ARG   0.003   0.000   ARG A 422 

*********************** 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
  134 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 85
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8708 (tppt) cc_final: 0.8237 (ttmt)
REVERT: B   19 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6947 (m-80)
REVERT: B  114 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8097 (pp20)
REVERT: B  344 LEU cc_start: 0.2047 (OUTLIER) cc_final: 0.1668 (mt)
  outliers start: 49
  outliers final: 33
  residues processed: 128
  average time/residue: 0.1629
  time to fit residues: 30.3947
Evaluate side-chains
  117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 81
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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  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  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   15 TYR
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  290 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  503 THR
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:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3880 r_free = 0.3880 target = 0.170204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.154494 restraints weight = 8661.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.136817 restraints weight = 15142.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.134287 restraints weight = 16042.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8244  Z= 0.294
  Angle     :  0.604   8.984  11192  Z= 0.313
  Chirality :  0.046   0.208   1267
  Planarity :  0.004   0.035   1438
  Dihedral  :  5.331  56.346   1109
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.00 %
    Favored  : 87.91 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.16 %
    Favored  : 73.12 %
  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: -4.14 (0.23), residues: 1017
  helix: -3.12 (0.27), residues: 241
  sheet: -2.89 (0.30), residues: 239
  loop : -2.45 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 258 
 PHE   0.013   0.001   PHE B  96 
 TYR   0.022   0.002   TYR B  19 
 ARG   0.004   0.000   ARG A 297 

*********************** 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
  124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 82
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8622 (tppt) cc_final: 0.8139 (ttmt)
REVERT: B   19 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6674 (m-80)
REVERT: B  114 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8129 (pp20)
REVERT: B  344 LEU cc_start: 0.2233 (OUTLIER) cc_final: 0.1961 (mt)
  outliers start: 42
  outliers final: 30
  residues processed: 117
  average time/residue: 0.1705
  time to fit residues: 28.7900
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
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  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   15 TYR
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 95 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   chunk 38 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:
** 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 = 0.3882 r_free = 0.3882 target = 0.170606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.157571 restraints weight = 8811.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.155122 restraints weight = 11553.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.153264 restraints weight = 16842.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8244  Z= 0.267
  Angle     :  0.590  11.111  11192  Z= 0.307
  Chirality :  0.045   0.207   1267
  Planarity :  0.004   0.033   1438
  Dihedral  :  5.219  54.619   1109
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.60 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.50 %
    Favored  : 72.89 %
  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: -4.06 (0.23), residues: 1017
  helix: -3.09 (0.27), residues: 241
  sheet: -2.83 (0.31), residues: 235
  loop : -2.40 (0.24), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.014   0.001   PHE B  96 
 TYR   0.018   0.002   TYR B  19 
 ARG   0.002   0.000   ARG A 352 

*********************** 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
  123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 82
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8524 (tppt) cc_final: 0.8118 (ttmt)
REVERT: B   19 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6683 (m-80)
REVERT: B   26 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7155 (m170)
REVERT: B  114 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8161 (pp20)
REVERT: B  344 LEU cc_start: 0.2731 (OUTLIER) cc_final: 0.2392 (mt)
  outliers start: 41
  outliers final: 29
  residues processed: 114
  average time/residue: 0.1794
  time to fit residues: 29.6548
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  276 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
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   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  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  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:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0060
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 57 optimal weight:    0.0270
   chunk 45 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.3854

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3903 r_free = 0.3903 target = 0.172728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.155742 restraints weight = 8590.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.154501 restraints weight = 14930.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.154086 restraints weight = 15363.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8244  Z= 0.175
  Angle     :  0.566  10.790  11192  Z= 0.290
  Chirality :  0.044   0.202   1267
  Planarity :  0.003   0.030   1438
  Dihedral  :  4.927  52.184   1109
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.52 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.28 %
    Favored  : 73.00 %
  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: -3.92 (0.23), residues: 1017
  helix: -2.86 (0.28), residues: 239
  sheet: -2.79 (0.31), residues: 235
  loop : -2.35 (0.24), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 299 
 HIS   0.003   0.000   HIS B  59 
 PHE   0.010   0.001   PHE B  96 
 TYR   0.015   0.002   TYR B 119 
 ARG   0.002   0.000   ARG B 318 

********************** 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
  113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8543 (tppt) cc_final: 0.8138 (ttmt)
REVERT: B   19 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6541 (m-80)
REVERT: B   26 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7142 (m170)
REVERT: B  114 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8162 (pp20)
REVERT: B  344 LEU cc_start: 0.2686 (OUTLIER) cc_final: 0.2369 (mt)
REVERT: B  383 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6905 (pp)
  outliers start: 33
  outliers final: 25
  residues processed: 106
  average time/residue: 0.2014
  time to fit residues: 31.6160
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  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  265 ILE
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  476 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   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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0010
   chunk 76 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 101 optimal weight:    0.0270
   chunk 45 optimal weight:    6.9990
   chunk 54 optimal weight:    0.3980
   overall best weight:    0.3444

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3930 r_free = 0.3930 target = 0.175252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.161476 restraints weight = 8606.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.158864 restraints weight = 14035.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.157811 restraints weight = 15516.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8244  Z= 0.160
  Angle     :  0.563  12.660  11192  Z= 0.286
  Chirality :  0.043   0.187   1267
  Planarity :  0.003   0.031   1438
  Dihedral  :  4.711  49.844   1109
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.23 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.85 %
    Favored  : 72.44 %
  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: -3.71 (0.23), residues: 1017
  helix: -2.62 (0.29), residues: 239
  sheet: -2.63 (0.33), residues: 208
  loop : -2.33 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 299 
 HIS   0.003   0.000   HIS B  59 
 PHE   0.009   0.001   PHE B  96 
 TYR   0.014   0.001   TYR B 119 
 ARG   0.003   0.000   ARG B 296 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2732.80 seconds
wall clock time: 50 minutes 17.13 seconds (3017.13 seconds total)