Starting phenix.real_space_refine
on Sat Aug 23 02:21:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1r_41825/08_2025/8u1r_41825_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1r_41825/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1r_41825/08_2025/8u1r_41825_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1r_41825/08_2025/8u1r_41825_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1r_41825/08_2025/8u1r_41825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1r_41825/08_2025/8u1r_41825.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.81, per 1000 atoms: 0.20
  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: 0.59
  Conformation dependent library (CDL) restraints added in 248.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.31
  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: 1.24

  Time building geometry restraints manager: 0.76 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: 0.01
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:             1.050
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.620
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.840
-------------------------------------------------------------------------------
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   9261  Z= 0.275
  Angle     :  0.775  10.223  12606  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.013   0.001   ARG A 360 
 TYR   0.017   0.002   TYR C 415 
 PHE   0.012   0.001   PHE B 234 
 TRP   0.009   0.002   TRP B 303 
 HIS   0.005   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 9243)
  covalent geometry    : angle       0.77448 (12570)
  SS BOND              : bond        0.00543 (   18)
  SS BOND              : angle       1.01663 (   36)
  hydrogen bonds       : bond        0.20661 (  459)
  hydrogen bonds       : angle       7.56304 ( 1269)

*********************** 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  : 0.421 
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: 0.1145
  time to fit residues: 22.1287
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  : 0.423 
-------------------------------------------------------------------------------
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 108 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   overall best weight:    1.1562

-------------------------------------------------------------------------------
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 381 ASN
C 384 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.120028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.100483 restraints weight = 11604.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.103427 restraints weight = 7216.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.105472 restraints weight = 5105.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.106892 restraints weight = 3976.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.107916 restraints weight = 3290.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9261  Z= 0.155
  Angle     :  0.575  10.821  12606  Z= 0.301
  Chirality :  0.044   0.167   1560
  Planarity :  0.004   0.035   1596
  Dihedral  :  5.307  56.854   1282
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.85 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.24), residues: 1185
  helix:  1.26 (0.26), residues: 411
  sheet:  0.14 (0.30), residues: 255
  loop : -0.83 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 360 
 TYR   0.014   0.002   TYR A 415 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.009   0.001   TRP B 303 
 HIS   0.006   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9243)
  covalent geometry    : angle       0.57441 (12570)
  SS BOND              : bond        0.00174 (   18)
  SS BOND              : angle       0.64163 (   36)
  hydrogen bonds       : bond        0.04505 (  459)
  hydrogen bonds       : angle       5.40119 ( 1269)

*********************** 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
  146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 MET cc_start: 0.8072 (mmp) cc_final: 0.7754 (ttt)
REVERT: B  390 MET cc_start: 0.7773 (mmp) cc_final: 0.7001 (ttt)
REVERT: C  325 ARG cc_start: 0.8288 (mtm110) cc_final: 0.8063 (mtm180)
REVERT: C  329 THR cc_start: 0.9120 (p) cc_final: 0.8918 (t)
REVERT: C  390 MET cc_start: 0.7434 (mmp) cc_final: 0.6721 (ttt)
REVERT: C  399 SER cc_start: 0.7064 (m) cc_final: 0.6659 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1003
  time to fit residues: 19.0456
Evaluate side-chains
  117 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  168 ASP
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 90 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    1.3188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.130280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.112005 restraints weight = 11416.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.114741 restraints weight = 7378.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.116681 restraints weight = 5377.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.118054 restraints weight = 4238.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.119003 restraints weight = 3526.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9261  Z= 0.163
  Angle     :  0.562   7.784  12606  Z= 0.293
  Chirality :  0.044   0.159   1560
  Planarity :  0.003   0.032   1596
  Dihedral  :  4.807  30.402   1276
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.66 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.24), residues: 1185
  helix:  1.38 (0.26), residues: 414
  sheet:  0.04 (0.28), residues: 285
  loop : -0.81 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 360 
 TYR   0.010   0.001   TYR C 249 
 PHE   0.016   0.002   PHE C 234 
 TRP   0.006   0.001   TRP B 303 
 HIS   0.005   0.002   HIS B 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9243)
  covalent geometry    : angle       0.55997 (12570)
  SS BOND              : bond        0.00283 (   18)
  SS BOND              : angle       1.07432 (   36)
  hydrogen bonds       : bond        0.04102 (  459)
  hydrogen bonds       : angle       5.09154 ( 1269)

*********************** 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
  140 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  390 MET cc_start: 0.7755 (mmp) cc_final: 0.7172 (ttt)
REVERT: C  390 MET cc_start: 0.7336 (mmp) cc_final: 0.6695 (ttt)
  outliers start: 25
  outliers final: 14
  residues processed: 130
  average time/residue: 0.0771
  time to fit residues: 14.9079
Evaluate side-chains
  123 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
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  281 THR
Chi-restraints excluded: chain C residue  306 LEU
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 12 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0980
   chunk 25 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 15 optimal weight:    0.1980
   chunk 81 optimal weight:    0.2980
   chunk 114 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.137797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.119798 restraints weight = 11304.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.122624 restraints weight = 7147.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.124612 restraints weight = 5120.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.125919 restraints weight = 4014.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.127028 restraints weight = 3351.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9261  Z= 0.101
  Angle     :  0.500   6.737  12606  Z= 0.262
  Chirality :  0.042   0.155   1560
  Planarity :  0.003   0.035   1596
  Dihedral  :  4.540  31.024   1276
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.24), residues: 1185
  helix:  1.50 (0.26), residues: 432
  sheet:  0.08 (0.29), residues: 285
  loop : -0.57 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 360 
 TYR   0.011   0.001   TYR B 427 
 PHE   0.013   0.001   PHE B 234 
 TRP   0.004   0.001   TRP B 303 
 HIS   0.004   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9243)
  covalent geometry    : angle       0.49917 (12570)
  SS BOND              : bond        0.00164 (   18)
  SS BOND              : angle       0.73785 (   36)
  hydrogen bonds       : bond        0.03386 (  459)
  hydrogen bonds       : angle       4.75984 ( 1269)

*********************** 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
  152 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.414 
Fit side-chains
REVERT: B  390 MET cc_start: 0.7720 (mmp) cc_final: 0.7134 (ttt)
REVERT: C  271 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8098 (tt)
REVERT: C  390 MET cc_start: 0.7256 (mmp) cc_final: 0.6541 (ttt)
  outliers start: 29
  outliers final: 12
  residues processed: 141
  average time/residue: 0.0845
  time to fit residues: 17.6636
Evaluate side-chains
  117 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
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  271 ILE
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 65 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 57 optimal weight:    0.9980
   chunk 3 optimal weight:    0.1980
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.134406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.116152 restraints weight = 11249.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.118979 restraints weight = 7241.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.120945 restraints weight = 5230.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.122256 restraints weight = 4137.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.123285 restraints weight = 3468.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9261  Z= 0.108
  Angle     :  0.515   7.104  12606  Z= 0.267
  Chirality :  0.043   0.172   1560
  Planarity :  0.003   0.034   1596
  Dihedral  :  4.365  23.161   1275
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.80 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.25), residues: 1185
  helix:  1.53 (0.26), residues: 432
  sheet: -0.15 (0.29), residues: 270
  loop : -0.35 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 360 
 TYR   0.011   0.001   TYR A 415 
 PHE   0.014   0.001   PHE B 234 
 TRP   0.004   0.001   TRP B 303 
 HIS   0.004   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9243)
  covalent geometry    : angle       0.51495 (12570)
  SS BOND              : bond        0.00155 (   18)
  SS BOND              : angle       0.67172 (   36)
  hydrogen bonds       : bond        0.03282 (  459)
  hydrogen bonds       : angle       4.68353 ( 1269)

*********************** 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
  144 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  110 MET cc_start: 0.8532 (tpt) cc_final: 0.8116 (tpt)
REVERT: B  390 MET cc_start: 0.7718 (mmp) cc_final: 0.7170 (ttt)
REVERT: C  390 MET cc_start: 0.7258 (mmp) cc_final: 0.6570 (ttt)
  outliers start: 26
  outliers final: 16
  residues processed: 131
  average time/residue: 0.0690
  time to fit residues: 14.4597
Evaluate side-chains
  127 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   52 MET
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  295 SER
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  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
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 30 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0570
   chunk 56 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.3372 r_free = 0.3372 target = 0.126936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.108137 restraints weight = 11413.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.110775 restraints weight = 7437.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.112738 restraints weight = 5467.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.114162 restraints weight = 4331.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.115053 restraints weight = 3638.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9261  Z= 0.112
  Angle     :  0.506   5.590  12606  Z= 0.264
  Chirality :  0.043   0.165   1560
  Planarity :  0.003   0.034   1596
  Dihedral  :  4.303  22.205   1275
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.19 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.25), residues: 1185
  helix:  1.60 (0.26), residues: 432
  sheet: -0.12 (0.29), residues: 270
  loop : -0.30 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 360 
 TYR   0.016   0.001   TYR B 379 
 PHE   0.014   0.001   PHE B 234 
 TRP   0.005   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9243)
  covalent geometry    : angle       0.50553 (12570)
  SS BOND              : bond        0.00143 (   18)
  SS BOND              : angle       0.60498 (   36)
  hydrogen bonds       : bond        0.03196 (  459)
  hydrogen bonds       : angle       4.58998 ( 1269)

*********************** 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
  148 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  110 MET cc_start: 0.8603 (tpt) cc_final: 0.8212 (tpt)
REVERT: A  200 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8201 (tt0)
REVERT: B  390 MET cc_start: 0.7804 (mmp) cc_final: 0.7128 (ttt)
REVERT: C  390 MET cc_start: 0.7349 (mmp) cc_final: 0.6575 (ttt)
  outliers start: 29
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0625
  time to fit residues: 13.8998
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  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  221 ILE
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  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 66 optimal weight:    0.0070
   chunk 3 optimal weight:    0.0970
   chunk 73 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0040
   chunk 37 optimal weight:    6.9990
   chunk 107 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.9810

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.121299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.102630 restraints weight = 11660.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.105042 restraints weight = 7766.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.106847 restraints weight = 5785.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.108083 restraints weight = 4663.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.108962 restraints weight = 3964.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9261  Z= 0.134
  Angle     :  0.531   7.007  12606  Z= 0.275
  Chirality :  0.044   0.162   1560
  Planarity :  0.003   0.034   1596
  Dihedral  :  4.342  22.339   1275
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1185
  helix:  1.63 (0.26), residues: 432
  sheet: -0.10 (0.30), residues: 270
  loop : -0.33 (0.29), residues: 483

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9243)
  covalent geometry    : angle       0.53035 (12570)
  SS BOND              : bond        0.00166 (   18)
  SS BOND              : angle       0.63908 (   36)
  hydrogen bonds       : bond        0.03309 (  459)
  hydrogen bonds       : angle       4.62018 ( 1269)

*********************** 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
  141 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.263 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8126 (tt0)
REVERT: B  390 MET cc_start: 0.7826 (mmp) cc_final: 0.7098 (ttt)
REVERT: C  390 MET cc_start: 0.7356 (mmp) cc_final: 0.6585 (ttt)
  outliers start: 29
  outliers final: 20
  residues processed: 128
  average time/residue: 0.0654
  time to fit residues: 13.4261
Evaluate side-chains
  128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   52 MET
Chi-restraints excluded: chain A residue  109 CYS
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  248 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 112 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  95 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.124379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.106031 restraints weight = 11478.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.108494 restraints weight = 7788.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.110277 restraints weight = 5830.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.111477 restraints weight = 4712.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.112400 restraints weight = 4024.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9261  Z= 0.127
  Angle     :  0.521   6.508  12606  Z= 0.270
  Chirality :  0.043   0.165   1560
  Planarity :  0.003   0.035   1596
  Dihedral  :  4.305  21.909   1275
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1185
  helix:  1.68 (0.26), residues: 432
  sheet: -0.13 (0.30), residues: 270
  loop : -0.28 (0.29), residues: 483

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9243)
  covalent geometry    : angle       0.52051 (12570)
  SS BOND              : bond        0.00164 (   18)
  SS BOND              : angle       0.59854 (   36)
  hydrogen bonds       : bond        0.03216 (  459)
  hydrogen bonds       : angle       4.58118 ( 1269)

*********************** 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
  143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.356 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8121 (tt0)
REVERT: B  390 MET cc_start: 0.7752 (mmp) cc_final: 0.7125 (ttt)
REVERT: C  390 MET cc_start: 0.7219 (mmp) cc_final: 0.6556 (ttt)
  outliers start: 28
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0624
  time to fit residues: 13.4366
Evaluate side-chains
  130 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
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  248 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0070
   chunk 44 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.8802

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.129030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.110131 restraints weight = 11431.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.112846 restraints weight = 7392.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114827 restraints weight = 5427.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.116095 restraints weight = 4293.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.117169 restraints weight = 3634.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9261  Z= 0.127
  Angle     :  0.531   9.396  12606  Z= 0.273
  Chirality :  0.044   0.172   1560
  Planarity :  0.003   0.035   1596
  Dihedral  :  4.308  22.208   1275
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1185
  helix:  1.72 (0.26), residues: 432
  sheet: -0.16 (0.30), residues: 270
  loop : -0.30 (0.29), residues: 483

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9243)
  covalent geometry    : angle       0.53127 (12570)
  SS BOND              : bond        0.00152 (   18)
  SS BOND              : angle       0.59394 (   36)
  hydrogen bonds       : bond        0.03201 (  459)
  hydrogen bonds       : angle       4.57061 ( 1269)

*********************** 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
  136 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.369 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8127 (tt0)
REVERT: B  390 MET cc_start: 0.7802 (mmp) cc_final: 0.7116 (ttt)
REVERT: C  330 GLU cc_start: 0.7749 (pm20) cc_final: 0.7481 (pm20)
REVERT: C  390 MET cc_start: 0.7193 (mmp) cc_final: 0.6453 (ttt)
  outliers start: 25
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0622
  time to fit residues: 12.6970
Evaluate side-chains
  133 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  115 LEU
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  164 LEU
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  248 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 115 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.123921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.105293 restraints weight = 11511.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.107766 restraints weight = 7664.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.109641 restraints weight = 5704.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.110930 restraints weight = 4567.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.111802 restraints weight = 3885.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9261  Z= 0.121
  Angle     :  0.526   9.242  12606  Z= 0.270
  Chirality :  0.043   0.165   1560
  Planarity :  0.003   0.036   1596
  Dihedral  :  4.259  21.758   1275
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1185
  helix:  1.77 (0.26), residues: 432
  sheet: -0.17 (0.30), residues: 270
  loop : -0.29 (0.29), residues: 483

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9243)
  covalent geometry    : angle       0.52593 (12570)
  SS BOND              : bond        0.00149 (   18)
  SS BOND              : angle       0.57196 (   36)
  hydrogen bonds       : bond        0.03134 (  459)
  hydrogen bonds       : angle       4.52712 ( 1269)

********************** 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
  137 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.380 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8125 (tt0)
REVERT: B  390 MET cc_start: 0.7842 (mmp) cc_final: 0.7136 (ttt)
REVERT: C  390 MET cc_start: 0.7125 (mmp) cc_final: 0.6400 (ttt)
  outliers start: 23
  outliers final: 21
  residues processed: 127
  average time/residue: 0.0680
  time to fit residues: 13.7282
Evaluate side-chains
  132 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   52 MET
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  248 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.123934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.105466 restraints weight = 11340.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.107897 restraints weight = 7547.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.109715 restraints weight = 5624.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.111043 restraints weight = 4514.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.111955 restraints weight = 3827.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9261  Z= 0.120
  Angle     :  0.531   9.396  12606  Z= 0.270
  Chirality :  0.043   0.160   1560
  Planarity :  0.003   0.035   1596
  Dihedral  :  4.235  21.801   1275
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.91 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.25), residues: 1185
  helix:  1.78 (0.26), residues: 432
  sheet: -0.17 (0.30), residues: 270
  loop : -0.28 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 360 
 TYR   0.020   0.001   TYR A 427 
 PHE   0.015   0.001   PHE C 234 
 TRP   0.004   0.001   TRP B 303 
 HIS   0.004   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9243)
  covalent geometry    : angle       0.53060 (12570)
  SS BOND              : bond        0.00144 (   18)
  SS BOND              : angle       0.57219 (   36)
  hydrogen bonds       : bond        0.03122 (  459)
  hydrogen bonds       : angle       4.51372 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1360.01 seconds
wall clock time: 24 minutes 19.46 seconds (1459.46 seconds total)