Starting phenix.real_space_refine
on Thu Feb 13 15:50:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1r_41825/02_2025/8u1r_41825_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1r_41825/02_2025/8u1r_41825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1r_41825/02_2025/8u1r_41825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1r_41825/02_2025/8u1r_41825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1r_41825/02_2025/8u1r_41825_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1r_41825/02_2025/8u1r_41825_neut.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.039
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      60      5.16       5
     C    5763      2.51       5
     N    1524      2.21       5
     O    1779      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9126
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3042
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 13, 'TRANS': 385}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3042
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 13, 'TRANS': 385}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3042
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 13, 'TRANS': 385}
          Chain breaks: 1
  Time building chain proxies: 5.05, per 1000 atoms: 0.55
  Number of scatterers: 9126
  At special positions: 0
  Unit cell: (100.58, 102.46, 94, 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      60     16.00
     O    1779      8.00
     N    1524      7.00
     C    5763      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 109 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 412 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  99 " - pdb=" SG  CYS B 109 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  99 " - pdb=" SG  CYS C 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 389 " - pdb=" SG  CYS C 412 " 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: 2.14
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2250

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 15 sheets defined
      41.4% alpha, 29.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 67 through 99
      removed outlier: 3.559A  pdb=" N   ASP A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      Proline residue:  A  84  - end of helix
      removed outlier: 4.146A  pdb=" N   CYS A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 3.552A  pdb=" N   LEU A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 132 through 141
    Processing helix  chain 'A' and resid 142 through 148
    Processing helix  chain 'A' and resid 168 through 178
    Processing helix  chain 'A' and resid 179 through 182
    Processing helix  chain 'A' and resid 186 through 209
    Processing helix  chain 'A' and resid 209 through 214
      removed outlier: 3.699A  pdb=" N   GLN A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 228
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 233 through 241
    Processing helix  chain 'A' and resid 248 through 253
    Processing helix  chain 'A' and resid 344 through 353
    Processing helix  chain 'A' and resid 354 through 358
    Processing helix  chain 'B' and resid 24 through 32
    Processing helix  chain 'B' and resid 60 through 64
      removed outlier: 3.804A  pdb=" N   ARG B  64 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 98
      Proline residue:  B  84  - end of helix
      removed outlier: 3.585A  pdb=" N   VAL B  96 " --> pdb=" O   MET B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 116
    Processing helix  chain 'B' and resid 120 through 142
      removed outlier: 4.468A  pdb=" N   GLU B 134 " --> pdb=" O   HIS B 130 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   ASN B 135 " --> pdb=" O   ARG B 131 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   MET B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 148
    Processing helix  chain 'B' and resid 168 through 178
    Processing helix  chain 'B' and resid 179 through 182
    Processing helix  chain 'B' and resid 186 through 209
    Processing helix  chain 'B' and resid 209 through 214
    Processing helix  chain 'B' and resid 223 through 228
    Processing helix  chain 'B' and resid 229 through 231
      No H-bonds generated for 'chain 'B' and resid 229 through 231'
    Processing helix  chain 'B' and resid 233 through 241
    Processing helix  chain 'B' and resid 248 through 254
      removed outlier: 4.309A  pdb=" N   SER B 254 " --> pdb=" O   GLU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 353
    Processing helix  chain 'B' and resid 354 through 358
    Processing helix  chain 'C' and resid 24 through 32
    Processing helix  chain 'C' and resid 60 through 64
      removed outlier: 3.794A  pdb=" N   ARG C  64 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 99
      removed outlier: 3.539A  pdb=" N   ASP C  72 " --> pdb=" O   GLN C  68 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  84  - end of helix
      removed outlier: 4.056A  pdb=" N   ASN C  95 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL C  96 " --> pdb=" O   MET C  92 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   CYS C  99 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.557A  pdb=" N   GLY C 116 " --> pdb=" O   GLY C 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 112 through 116'
    Processing helix  chain 'C' and resid 120 through 142
      removed outlier: 4.522A  pdb=" N   GLU C 134 " --> pdb=" O   HIS C 130 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ASN C 135 " --> pdb=" O   ARG C 131 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   MET C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 148
    Processing helix  chain 'C' and resid 168 through 178
    Processing helix  chain 'C' and resid 179 through 182
    Processing helix  chain 'C' and resid 186 through 209
    Processing helix  chain 'C' and resid 209 through 214
    Processing helix  chain 'C' and resid 223 through 228
    Processing helix  chain 'C' and resid 229 through 231
      No H-bonds generated for 'chain 'C' and resid 229 through 231'
    Processing helix  chain 'C' and resid 233 through 241
    Processing helix  chain 'C' and resid 248 through 254
      removed outlier: 4.146A  pdb=" N   SER C 254 " --> pdb=" O   GLU C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 353
    Processing helix  chain 'C' and resid 354 through 358
    Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 157
      removed outlier: 8.055A  pdb=" N   THR A 163 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU A  51 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   LYS A  35 " --> pdb=" O   MET A 292 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   MET A 292 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LEU A  37 " --> pdb=" O   GLU A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 265
      removed outlier: 6.351A  pdb=" N   GLY A 259 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   GLU A 276 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ILE A 261 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   GLU A 274 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A 263 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASN A 279 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   SER A  46 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   THR A 281 " --> pdb=" O   LYS A  44 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   LYS A  44 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119
      removed outlier: 3.769A  pdb=" N   VAL B 378 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298
      removed outlier: 4.392A  pdb=" N   ALA A 359 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 407
      removed outlier: 3.871A  pdb=" N   VAL A 378 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388
      removed outlier: 3.710A  pdb=" N   MET C 110 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 157
      removed outlier: 8.054A  pdb=" N   THR B 163 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU B  51 " --> pdb=" O   THR B 163 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   VAL B 333 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASN B  40 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   CYS B 335 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   LYS B  42 " --> pdb=" O   CYS B 335 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.911A  pdb=" N   ARG B 258 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ALA B 272 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   VAL B 264 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   TYR B 270 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN B 279 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   SER B  46 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   THR B 281 " --> pdb=" O   LYS B  44 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   LYS B  44 " --> pdb=" O   THR B 281 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   LYS B  35 " --> pdb=" O   MET B 292 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   MET B 292 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   LEU B  37 " --> pdb=" O   GLU B 290 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   PHE B 310 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ILE B 321 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111
      removed outlier: 6.800A  pdb=" N   MET B 110 " --> pdb=" O   SER C 423 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 117 through 119
      removed outlier: 3.802A  pdb=" N   VAL C 378 " --> pdb=" O   LEU C 407 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU C 407 " --> pdb=" O   VAL C 378 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298
      removed outlier: 4.589A  pdb=" N   ALA B 359 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 389
    Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 157
      removed outlier: 8.159A  pdb=" N   THR C 163 " --> pdb=" O   THR C  49 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU C  51 " --> pdb=" O   THR C 163 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222
      removed outlier: 4.108A  pdb=" N   ARG C 258 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   VAL C 264 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   TYR C 270 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASN C 279 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   SER C  46 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   THR C 281 " --> pdb=" O   LYS C  44 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   LYS C  44 " --> pdb=" O   THR C 281 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   GLU C 290 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   THR C  38 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   VAL C 288 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   PHE C 310 " --> pdb=" O   ILE C 321 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ILE C 321 " --> pdb=" O   PHE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298
      removed outlier: 4.486A  pdb=" N   ALA C 359 " --> pdb=" O   LEU C 306 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1269 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: 2.74

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2994
        1.34 -     1.46: 1468
        1.46 -     1.58: 4697
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 9243
  Sorted by residual:
  bond pdb=" N   ILE C 422 "
       pdb=" CA  ILE C 422 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.11e-02 8.12e+03 1.23e+01
  bond pdb=" N   ILE B 422 "
       pdb=" CA  ILE B 422 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.038 1.14e-02 7.69e+03 1.12e+01
  bond pdb=" N   ILE B 420 "
       pdb=" CA  ILE B 420 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.12e-02 7.97e+03 1.06e+01
  bond pdb=" CA  SER A 423 "
       pdb=" CB  SER A 423 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.048 1.61e-02 3.86e+03 9.07e+00
  bond pdb=" N   VAL B  96 "
       pdb=" CA  VAL B  96 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.28e-02 6.10e+03 8.91e+00
  ... (remaining 9238 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 12180
        2.04 -     4.09: 344
        4.09 -     6.13: 39
        6.13 -     8.18: 5
        8.18 -    10.22: 2
  Bond angle restraints: 12570
  Sorted by residual:
  angle pdb=" C   CYS A 387 "
        pdb=" N   ARG A 388 "
        pdb=" CA  ARG A 388 "
      ideal   model   delta    sigma   weight residual
     122.36  116.09    6.27 1.60e+00 3.91e-01 1.54e+01
  angle pdb=" CA  SER A 423 "
        pdb=" C   SER A 423 "
        pdb=" O   SER A 423 "
      ideal   model   delta    sigma   weight residual
     121.94  117.66    4.28 1.15e+00 7.56e-01 1.39e+01
  angle pdb=" N   MET A 390 "
        pdb=" CA  MET A 390 "
        pdb=" C   MET A 390 "
      ideal   model   delta    sigma   weight residual
     112.38  107.89    4.49 1.22e+00 6.72e-01 1.36e+01
  angle pdb=" CA  ILE C 422 "
        pdb=" C   ILE C 422 "
        pdb=" O   ILE C 422 "
      ideal   model   delta    sigma   weight residual
     121.67  117.85    3.82 1.05e+00 9.07e-01 1.32e+01
  angle pdb=" N   VAL A  31 "
        pdb=" CA  VAL A  31 "
        pdb=" C   VAL A  31 "
      ideal   model   delta    sigma   weight residual
     113.39  108.07    5.32 1.47e+00 4.63e-01 1.31e+01
  ... (remaining 12565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 5101
       17.85 -    35.71: 450
       35.71 -    53.56: 114
       53.56 -    71.41: 19
       71.41 -    89.26: 19
  Dihedral angle restraints: 5703
    sinusoidal: 2214
      harmonic: 3489
  Sorted by residual:
  dihedral pdb=" CB  CYS C 389 "
           pdb=" SG  CYS C 389 "
           pdb=" SG  CYS C 412 "
           pdb=" CB  CYS C 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -170.97   84.97     1      1.00e+01 1.00e-02 8.76e+01
  dihedral pdb=" CB  CYS A  66 "
           pdb=" SG  CYS A  66 "
           pdb=" SG  CYS A 187 "
           pdb=" CB  CYS A 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.15   38.15     1      1.00e+01 1.00e-02 2.05e+01
  dihedral pdb=" CB  CYS C  66 "
           pdb=" SG  CYS C  66 "
           pdb=" SG  CYS C 187 "
           pdb=" CB  CYS C 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.93   37.93     1      1.00e+01 1.00e-02 2.03e+01
  ... (remaining 5700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1213
       0.053 -    0.107: 263
       0.107 -    0.160: 67
       0.160 -    0.214: 14
       0.214 -    0.267: 3
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CA  ILE A 422 "
            pdb=" N   ILE A 422 "
            pdb=" C   ILE A 422 "
            pdb=" CB  ILE A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CA  ILE C 422 "
            pdb=" N   ILE C 422 "
            pdb=" C   ILE C 422 "
            pdb=" CB  ILE C 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  ILE B 422 "
            pdb=" N   ILE B 422 "
            pdb=" C   ILE B 422 "
            pdb=" CB  ILE B 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1557 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  90 "    0.029 2.00e-02 2.50e+03   5.71e-02 3.26e+01
        pdb=" C   ASN A  90 "   -0.099 2.00e-02 2.50e+03
        pdb=" O   ASN A  90 "    0.037 2.00e-02 2.50e+03
        pdb=" N   ALA A  91 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 419 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.65e+00
        pdb=" CG  ASP A 419 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 419 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 419 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  57 "   -0.030 5.00e-02 4.00e+02   4.49e-02 3.22e+00
        pdb=" N   PRO A  58 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 401
        2.73 -     3.27: 9226
        3.27 -     3.81: 14383
        3.81 -     4.36: 17385
        4.36 -     4.90: 29620
  Nonbonded interactions: 71015
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  41 "
            pdb=" O   ASP C 338 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OH  TYR B  41 "
            pdb=" O   ASP B 338 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" O   ASP A 338 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR C 329 "
            pdb=" O   SER C 332 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OD1 ASP A 338 "
            pdb=" OG  SER B 365 "
     model   vdw
     2.330 3.040
  ... (remaining 71010 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.980
  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:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
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      :  0.005   0.048   9243  Z= 0.292
  Angle     :  0.774  10.223  12570  Z= 0.471
  Chirality :  0.051   0.267   1560
  Planarity :  0.004   0.057   1596
  Dihedral  : 15.163  89.263   3399
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.75 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.23), residues: 1185
  helix:  0.62 (0.25), residues: 417
  sheet:  0.14 (0.31), residues: 252
  loop : -0.97 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 303 
 HIS   0.005   0.001   HIS A 130 
 PHE   0.012   0.001   PHE B 234 
 TYR   0.017   0.002   TYR C 415 
 ARG   0.013   0.001   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 MET cc_start: 0.8080 (mmp) cc_final: 0.7742 (ttt)
REVERT: A  399 SER cc_start: 0.6967 (m) cc_final: 0.6452 (p)
REVERT: B  390 MET cc_start: 0.7562 (mmp) cc_final: 0.6877 (ttp)
REVERT: C  390 MET cc_start: 0.7399 (mmp) cc_final: 0.6865 (ttp)
REVERT: C  399 SER cc_start: 0.6770 (m) cc_final: 0.6222 (p)
  outliers start: 11
  outliers final: 3
  residues processed: 141
  average time/residue: 0.2270
  time to fit residues: 44.0501
Evaluate side-chains
  123 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  110 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B 381 ASN
B 384 ASN
C 157 GLN
C 381 ASN
C 384 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.127763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.109947 restraints weight = 11471.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.112443 restraints weight = 7680.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.114277 restraints weight = 5722.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9243  Z= 0.310
  Angle     :  0.608  10.584  12570  Z= 0.318
  Chirality :  0.045   0.168   1560
  Planarity :  0.004   0.035   1596
  Dihedral  :  5.406  57.316   1282
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.33 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1185
  helix:  1.16 (0.26), residues: 411
  sheet:  0.10 (0.28), residues: 285
  loop : -0.88 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 303 
 HIS   0.006   0.002   HIS C 130 
 PHE   0.016   0.002   PHE B 234 
 TYR   0.012   0.002   TYR A 415 
 ARG   0.006   0.001   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  367 TYR cc_start: 0.7259 (t80) cc_final: 0.6927 (t80)
REVERT: B  390 MET cc_start: 0.7654 (mmp) cc_final: 0.7073 (ttt)
REVERT: C  325 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7990 (mtm180)
REVERT: C  390 MET cc_start: 0.7316 (mmp) cc_final: 0.6783 (ttt)
REVERT: C  399 SER cc_start: 0.7076 (m) cc_final: 0.6748 (p)
  outliers start: 17
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2200
  time to fit residues: 42.0480
Evaluate side-chains
  114 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  321 ILE
Chi-restraints excluded: chain C residue  368 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0050
   chunk 98 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0000
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7402

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.135402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.117891 restraints weight = 11368.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.120538 restraints weight = 7380.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.122444 restraints weight = 5388.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9243  Z= 0.178
  Angle     :  0.530   7.872  12570  Z= 0.278
  Chirality :  0.043   0.159   1560
  Planarity :  0.003   0.033   1596
  Dihedral  :  4.757  30.381   1276
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.75 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1185
  helix:  1.47 (0.26), residues: 414
  sheet:  0.10 (0.29), residues: 285
  loop : -0.78 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.015   0.001   PHE C 234 
 TYR   0.009   0.001   TYR A 296 
 ARG   0.006   0.001   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 1.065 
Fit side-chains
REVERT: B  390 MET cc_start: 0.7781 (mmp) cc_final: 0.7194 (ttt)
REVERT: C  271 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8282 (tt)
REVERT: C  390 MET cc_start: 0.7336 (mmp) cc_final: 0.6679 (ttt)
  outliers start: 28
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1802
  time to fit residues: 36.1809
Evaluate side-chains
  120 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  368 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0570
   chunk 42 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 32 optimal weight:    0.3980
   chunk 99 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
C 253 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.135261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.117171 restraints weight = 11237.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.119960 restraints weight = 7184.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.122002 restraints weight = 5176.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9243  Z= 0.159
  Angle     :  0.510   6.723  12570  Z= 0.266
  Chirality :  0.043   0.154   1560
  Planarity :  0.003   0.034   1596
  Dihedral  :  4.575  30.893   1276
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.37 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.24), residues: 1185
  helix:  1.48 (0.26), residues: 432
  sheet:  0.10 (0.29), residues: 285
  loop : -0.55 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 303 
 HIS   0.004   0.001   HIS C 130 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.009   0.001   TYR C 415 
 ARG   0.006   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.995 
Fit side-chains
REVERT: A  110 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8042 (tpt)
REVERT: A  420 ILE cc_start: 0.8598 (tt) cc_final: 0.8311 (pt)
REVERT: B  390 MET cc_start: 0.7809 (mmp) cc_final: 0.7144 (ttt)
REVERT: C  390 MET cc_start: 0.7375 (mmp) cc_final: 0.6582 (ttt)
  outliers start: 31
  outliers final: 15
  residues processed: 136
  average time/residue: 0.1466
  time to fit residues: 31.5822
Evaluate side-chains
  119 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  408 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 85 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 253 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.122000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.103434 restraints weight = 11448.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.105749 restraints weight = 7645.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.107660 restraints weight = 5758.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9243  Z= 0.183
  Angle     :  0.519   9.551  12570  Z= 0.268
  Chirality :  0.043   0.166   1560
  Planarity :  0.003   0.035   1596
  Dihedral  :  4.408  22.542   1275
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.52 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1185
  helix:  1.51 (0.26), residues: 432
  sheet: -0.09 (0.30), residues: 270
  loop : -0.32 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.009   0.001   TYR C 249 
 ARG   0.004   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  110 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8096 (tpt)
REVERT: B  390 MET cc_start: 0.7834 (mmp) cc_final: 0.7181 (ttt)
REVERT: C  390 MET cc_start: 0.7416 (mmp) cc_final: 0.6673 (ttt)
  outliers start: 30
  outliers final: 18
  residues processed: 133
  average time/residue: 0.1455
  time to fit residues: 30.8047
Evaluate side-chains
  131 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  408 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0170
   chunk 9 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 72 optimal weight:    0.1980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
C 253 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.124227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.105694 restraints weight = 11355.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.108156 restraints weight = 7592.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.110066 restraints weight = 5661.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9243  Z= 0.155
  Angle     :  0.498   6.953  12570  Z= 0.260
  Chirality :  0.043   0.165   1560
  Planarity :  0.003   0.036   1596
  Dihedral  :  4.305  22.254   1275
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.47 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1185
  helix:  1.61 (0.26), residues: 432
  sheet: -0.07 (0.30), residues: 270
  loop : -0.24 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.014   0.001   TYR B 379 
 ARG   0.004   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 1.039 
Fit side-chains
REVERT: B  390 MET cc_start: 0.7834 (mmp) cc_final: 0.7143 (ttt)
REVERT: C  110 MET cc_start: 0.8067 (tpt) cc_final: 0.7843 (tpt)
REVERT: C  390 MET cc_start: 0.7342 (mmp) cc_final: 0.6549 (ttt)
  outliers start: 27
  outliers final: 17
  residues processed: 135
  average time/residue: 0.1429
  time to fit residues: 31.0453
Evaluate side-chains
  123 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  408 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 115 optimal weight:   10.0000
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 253 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.124655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.105838 restraints weight = 11575.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.108435 restraints weight = 7721.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.110239 restraints weight = 5717.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9243  Z= 0.192
  Angle     :  0.525   8.234  12570  Z= 0.269
  Chirality :  0.043   0.138   1560
  Planarity :  0.003   0.035   1596
  Dihedral  :  4.313  22.353   1275
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.57 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1185
  helix:  1.65 (0.26), residues: 432
  sheet: -0.12 (0.29), residues: 270
  loop : -0.26 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 303 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.016   0.001   TYR B 379 
 ARG   0.004   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 1.019 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8152 (tt0)
REVERT: B  390 MET cc_start: 0.7835 (mmp) cc_final: 0.7136 (ttt)
REVERT: C  390 MET cc_start: 0.7354 (mmp) cc_final: 0.6578 (ttt)
  outliers start: 27
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1561
  time to fit residues: 31.1516
Evaluate side-chains
  128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  392 THR
Chi-restraints excluded: chain C residue  408 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0270
   chunk 76 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0010
   chunk 28 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.4244

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

Flipped N/Q/H residues before XYZ refinement:
C 253 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.124287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.105291 restraints weight = 11616.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.107715 restraints weight = 7736.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.109670 restraints weight = 5786.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9243  Z= 0.141
  Angle     :  0.505   8.094  12570  Z= 0.259
  Chirality :  0.042   0.156   1560
  Planarity :  0.003   0.039   1596
  Dihedral  :  4.172  21.744   1275
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.05 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.25), residues: 1185
  helix:  1.77 (0.26), residues: 432
  sheet: -0.09 (0.30), residues: 270
  loop : -0.19 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 303 
 HIS   0.005   0.001   HIS B 130 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.015   0.001   TYR B 379 
 ARG   0.003   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 1.000 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8203 (tt0)
REVERT: B  390 MET cc_start: 0.7893 (mmp) cc_final: 0.7095 (ttt)
REVERT: C  390 MET cc_start: 0.7284 (mmp) cc_final: 0.6508 (ttt)
  outliers start: 24
  outliers final: 17
  residues processed: 133
  average time/residue: 0.1648
  time to fit residues: 34.4321
Evaluate side-chains
  129 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  392 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0970
   chunk 92 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0030
   chunk 78 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
C 253 HIS
C 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.125512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.106929 restraints weight = 11390.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.109405 restraints weight = 7595.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.111088 restraints weight = 5648.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9243  Z= 0.148
  Angle     :  0.516  10.358  12570  Z= 0.261
  Chirality :  0.042   0.159   1560
  Planarity :  0.003   0.042   1596
  Dihedral  :  4.147  21.599   1275
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.33 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.25), residues: 1185
  helix:  1.84 (0.26), residues: 432
  sheet: -0.03 (0.30), residues: 270
  loop : -0.19 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.014   0.001   TYR C 415 
 ARG   0.003   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: B  200 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8187 (tt0)
REVERT: B  390 MET cc_start: 0.7901 (mmp) cc_final: 0.7080 (ttt)
REVERT: C  390 MET cc_start: 0.7222 (mmp) cc_final: 0.6441 (ttt)
  outliers start: 24
  outliers final: 19
  residues processed: 132
  average time/residue: 0.1506
  time to fit residues: 31.3448
Evaluate side-chains
  135 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:    0.3980
   chunk 96 optimal weight:    0.5980
   chunk 113 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  40 ASN
C 253 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.126548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.108185 restraints weight = 11505.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.110553 restraints weight = 7764.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.112467 restraints weight = 5846.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9243  Z= 0.162
  Angle     :  0.524  10.843  12570  Z= 0.262
  Chirality :  0.043   0.165   1560
  Planarity :  0.003   0.042   1596
  Dihedral  :  4.126  21.626   1275
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.43 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.25), residues: 1185
  helix:  1.86 (0.26), residues: 432
  sheet: -0.01 (0.30), residues: 270
  loop : -0.20 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 303 
 HIS   0.005   0.001   HIS B 130 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.018   0.001   TYR A 427 
 ARG   0.003   0.000   ARG A 360 

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: B  200 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8163 (tt0)
REVERT: B  390 MET cc_start: 0.7844 (mmp) cc_final: 0.7101 (ttt)
REVERT: C  390 MET cc_start: 0.7143 (mmp) cc_final: 0.6389 (ttt)
  outliers start: 22
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1593
  time to fit residues: 32.4678
Evaluate side-chains
  132 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  336 ASP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 ASP
Chi-restraints excluded: chain C residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   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  40 ASN
C 253 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.123923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.105211 restraints weight = 11541.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.107535 restraints weight = 7709.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.109413 restraints weight = 5795.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9243  Z= 0.180
  Angle     :  0.553  14.175  12570  Z= 0.271
  Chirality :  0.043   0.166   1560
  Planarity :  0.003   0.041   1596
  Dihedral  :  4.153  21.640   1275
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.81 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1185
  helix:  2.05 (0.26), residues: 414
  sheet: -0.02 (0.30), residues: 270
  loop : -0.26 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 303 
 HIS   0.005   0.001   HIS B 130 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.018   0.001   TYR A 427 
 ARG   0.003   0.000   ARG A 360 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2426.07 seconds
wall clock time: 44 minutes 46.78 seconds (2686.78 seconds total)