Starting phenix.real_space_refine
on Wed Feb  4 14:11:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e4f_47508/02_2026/9e4f_47508.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e4f_47508/02_2026/9e4f_47508.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e4f_47508/02_2026/9e4f_47508.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e4f_47508/02_2026/9e4f_47508.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e4f_47508/02_2026/9e4f_47508.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e4f_47508/02_2026/9e4f_47508.map"
  }
  resolution = 2.69
  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=   0.000 sd=   0.014
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      87      5.16       5
     C    6945      2.51       5
     N    1782      2.21       5
     O    2028      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10842
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3614
          Classifications: {'peptide': 451}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 432}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.24, per 1000 atoms: 0.21
  Number of scatterers: 10842
  At special positions: 0
  Unit cell: (96.485, 92.29, 131.723, 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      87     16.00
     O    2028      8.00
     N    1782      7.00
     C    6945      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 290 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 310 " - pdb=" SG  CYS A 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 314 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 325 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  93 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 172 " - pdb=" SG  CYS C 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 290 " - pdb=" SG  CYS B 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 290 " - pdb=" SG  CYS C 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 310 " - pdb=" SG  CYS B 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 310 " - pdb=" SG  CYS C 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 314 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 314 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 323 " - pdb=" SG  CYS B 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 323 " - pdb=" SG  CYS C 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 325 " - pdb=" SG  CYS B 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 325 " - pdb=" SG  CYS C 337 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 493.4 milliseconds
  

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 12 sheets defined
      42.4% alpha, 24.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 40 through 70
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.578A  pdb=" N   MET A 129 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA A 130 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 126 through 130'
    Processing helix  chain 'A' and resid 131 through 142
    Processing helix  chain 'A' and resid 153 through 162
    Processing helix  chain 'A' and resid 164 through 168
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 225 through 229
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 306 through 324
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 386 through 394
    Processing helix  chain 'A' and resid 397 through 404
      removed outlier: 3.718A  pdb=" N   GLY A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 403 " --> pdb=" O   GLN A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 443
    Processing helix  chain 'A' and resid 446 through 463
      removed outlier: 4.258A  pdb=" N   HIS A 463 " --> pdb=" O   GLU A 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 40 through 70
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.578A  pdb=" N   MET B 129 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA B 130 " --> pdb=" O   THR B 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 126 through 130'
    Processing helix  chain 'B' and resid 131 through 142
    Processing helix  chain 'B' and resid 153 through 162
    Processing helix  chain 'B' and resid 164 through 168
    Processing helix  chain 'B' and resid 180 through 182
      No H-bonds generated for 'chain 'B' and resid 180 through 182'
    Processing helix  chain 'B' and resid 225 through 229
    Processing helix  chain 'B' and resid 257 through 262
    Processing helix  chain 'B' and resid 306 through 324
    Processing helix  chain 'B' and resid 338 through 345
    Processing helix  chain 'B' and resid 345 through 355
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 397 through 404
      removed outlier: 3.718A  pdb=" N   GLY B 402 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU B 403 " --> pdb=" O   GLN B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 443
    Processing helix  chain 'B' and resid 446 through 463
      removed outlier: 4.258A  pdb=" N   HIS B 463 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 40 through 70
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 126 through 130
      removed outlier: 3.578A  pdb=" N   MET C 129 " --> pdb=" O   ASP C 126 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA C 130 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 126 through 130'
    Processing helix  chain 'C' and resid 131 through 142
    Processing helix  chain 'C' and resid 153 through 162
    Processing helix  chain 'C' and resid 164 through 168
    Processing helix  chain 'C' and resid 180 through 182
      No H-bonds generated for 'chain 'C' and resid 180 through 182'
    Processing helix  chain 'C' and resid 225 through 229
    Processing helix  chain 'C' and resid 257 through 262
    Processing helix  chain 'C' and resid 306 through 324
    Processing helix  chain 'C' and resid 338 through 345
    Processing helix  chain 'C' and resid 345 through 355
    Processing helix  chain 'C' and resid 386 through 394
    Processing helix  chain 'C' and resid 397 through 404
      removed outlier: 3.718A  pdb=" N   GLY C 402 " --> pdb=" O   GLU C 398 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU C 403 " --> pdb=" O   GLN C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 427 through 443
    Processing helix  chain 'C' and resid 446 through 463
      removed outlier: 4.258A  pdb=" N   HIS C 463 " --> pdb=" O   GLU C 459 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80
      removed outlier: 6.043A  pdb=" N   ASP A 223 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   LEU A 169 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 80
      removed outlier: 6.154A  pdb=" N   PHE A 269 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP A 409 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   THR A 271 " --> pdb=" O   ASP A 409 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   PHE A 411 " --> pdb=" O   THR A 271 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   VAL A 273 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   CYS A 275 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU A 415 " --> pdb=" O   CYS A 275 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   GLU A 277 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   TYR A 417 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   ARG A 279 " --> pdb=" O   TYR A 417 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR A 419 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ILE A 281 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU A 421 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189
      removed outlier: 7.140A  pdb=" N   LYS A 193 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   ASN A  94 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80
      removed outlier: 6.043A  pdb=" N   ASP B 223 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   LEU B 169 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 80
      removed outlier: 6.154A  pdb=" N   PHE B 269 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP B 409 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   THR B 271 " --> pdb=" O   ASP B 409 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   PHE B 411 " --> pdb=" O   THR B 271 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL B 273 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   GLU B 413 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   CYS B 275 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU B 415 " --> pdb=" O   CYS B 275 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   GLU B 277 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   TYR B 417 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   ARG B 279 " --> pdb=" O   TYR B 417 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR B 419 " --> pdb=" O   ARG B 279 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ILE B 281 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU B 421 " --> pdb=" O   ILE B 281 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86
    Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189
      removed outlier: 7.141A  pdb=" N   LYS B 193 " --> pdb=" O   ASN B  94 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   ASN B  94 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 80
      removed outlier: 6.044A  pdb=" N   ASP C 223 " --> pdb=" O   LEU C 169 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   LEU C 169 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 80
      removed outlier: 6.154A  pdb=" N   PHE C 269 " --> pdb=" O   VAL C 407 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ASP C 409 " --> pdb=" O   PHE C 269 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   THR C 271 " --> pdb=" O   ASP C 409 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   PHE C 411 " --> pdb=" O   THR C 271 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL C 273 " --> pdb=" O   PHE C 411 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLU C 413 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   CYS C 275 " --> pdb=" O   GLU C 413 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU C 415 " --> pdb=" O   CYS C 275 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   GLU C 277 " --> pdb=" O   LEU C 415 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   TYR C 417 " --> pdb=" O   GLU C 277 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   ARG C 279 " --> pdb=" O   TYR C 417 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR C 419 " --> pdb=" O   ARG C 279 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ILE C 281 " --> pdb=" O   THR C 419 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLU C 421 " --> pdb=" O   ILE C 281 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86
    Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189
      removed outlier: 7.140A  pdb=" N   LYS C 193 " --> pdb=" O   ASN C  94 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   ASN C  94 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)

    537 hydrogen bonds defined for protein.
    1530 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: 1.39

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3516
        1.35 -     1.46: 2634
        1.46 -     1.58: 4830
        1.58 -     1.70: 0
        1.70 -     1.82: 120
  Bond restraints: 11100
  Sorted by residual:
  bond pdb=" CA  GLU A  79 "
       pdb=" C   GLU A  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.010 1.08e-02 8.57e+03 8.67e-01
  bond pdb=" CA  GLU B  79 "
       pdb=" C   GLU B  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.010 1.08e-02 8.57e+03 8.60e-01
  bond pdb=" CA  GLU C  79 "
       pdb=" C   GLU C  79 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.010 1.08e-02 8.57e+03 8.41e-01
  bond pdb=" N   PRO C 285 "
       pdb=" CA  PRO C 285 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.31e-02 5.83e+03 8.11e-01
  bond pdb=" N   PRO A 285 "
       pdb=" CA  PRO A 285 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.31e-02 5.83e+03 7.59e-01
  ... (remaining 11095 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.90: 14203
        0.90 -     1.80: 669
        1.80 -     2.70: 93
        2.70 -     3.60: 35
        3.60 -     4.50: 9
  Bond angle restraints: 15009
  Sorted by residual:
  angle pdb=" N   ILE B 443 "
        pdb=" CA  ILE B 443 "
        pdb=" C   ILE B 443 "
      ideal   model   delta    sigma   weight residual
     113.47  110.50    2.97 1.01e+00 9.80e-01 8.65e+00
  angle pdb=" N   ILE A 443 "
        pdb=" CA  ILE A 443 "
        pdb=" C   ILE A 443 "
      ideal   model   delta    sigma   weight residual
     113.47  110.50    2.97 1.01e+00 9.80e-01 8.62e+00
  angle pdb=" N   ILE C 443 "
        pdb=" CA  ILE C 443 "
        pdb=" C   ILE C 443 "
      ideal   model   delta    sigma   weight residual
     113.47  110.53    2.94 1.01e+00 9.80e-01 8.47e+00
  angle pdb=" N   LYS A 464 "
        pdb=" CA  LYS A 464 "
        pdb=" C   LYS A 464 "
      ideal   model   delta    sigma   weight residual
     113.88  110.82    3.06 1.23e+00 6.61e-01 6.21e+00
  angle pdb=" N   LYS C 464 "
        pdb=" CA  LYS C 464 "
        pdb=" C   LYS C 464 "
      ideal   model   delta    sigma   weight residual
     113.88  110.83    3.05 1.23e+00 6.61e-01 6.17e+00
  ... (remaining 15004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 6095
       16.52 -    33.04: 442
       33.04 -    49.56: 111
       49.56 -    66.08: 42
       66.08 -    82.61: 15
  Dihedral angle restraints: 6705
    sinusoidal: 2742
      harmonic: 3963
  Sorted by residual:
  dihedral pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" SG  CYS A 179 "
           pdb=" CB  CYS A 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.26  -64.74     1      1.00e+01 1.00e-02 5.50e+01
  dihedral pdb=" CB  CYS C 172 "
           pdb=" SG  CYS C 172 "
           pdb=" SG  CYS C 179 "
           pdb=" CB  CYS C 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.29  -64.71     1      1.00e+01 1.00e-02 5.50e+01
  dihedral pdb=" CB  CYS B 172 "
           pdb=" SG  CYS B 172 "
           pdb=" SG  CYS B 179 "
           pdb=" CB  CYS B 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.31  -64.69     1      1.00e+01 1.00e-02 5.50e+01
  ... (remaining 6702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1053
       0.030 -    0.059: 434
       0.059 -    0.089: 75
       0.089 -    0.118: 51
       0.118 -    0.148: 7
  Chirality restraints: 1620
  Sorted by residual:
  chirality pdb=" CA  ILE B 124 "
            pdb=" N   ILE B 124 "
            pdb=" C   ILE B 124 "
            pdb=" CB  ILE B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CA  ILE C 124 "
            pdb=" N   ILE C 124 "
            pdb=" C   ILE C 124 "
            pdb=" CB  ILE C 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  ILE A 124 "
            pdb=" N   ILE A 124 "
            pdb=" C   ILE A 124 "
            pdb=" CB  ILE A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.20e-01
  ... (remaining 1617 not shown)

  Planarity restraints: 1944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 284 "   -0.017 5.00e-02 4.00e+02   2.54e-02 1.03e+00
        pdb=" N   PRO B 285 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 285 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 285 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 284 "    0.017 5.00e-02 4.00e+02   2.52e-02 1.02e+00
        pdb=" N   PRO A 285 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 284 "    0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO C 285 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO C 285 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 285 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1941 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2638
        2.79 -     3.32: 10441
        3.32 -     3.85: 18423
        3.85 -     4.37: 22458
        4.37 -     4.90: 38297
  Nonbonded interactions: 92257
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 318 "
            pdb=" ND2 ASN C 322 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   TYR B 318 "
            pdb=" ND2 ASN B 322 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   TYR A 318 "
            pdb=" ND2 ASN A 322 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OE2 GLU B 321 "
            pdb=" OH  TYR B 360 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE2 GLU C 321 "
            pdb=" OH  TYR C 360 "
     model   vdw
     2.302 3.040
  ... (remaining 92252 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: 0.02
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.590
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.620
  Find NCS groups from input model:        0.070
  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:6.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
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      :  0.002   0.014  11121  Z= 0.087
  Angle     :  0.451   4.497  15051  Z= 0.263
  Chirality :  0.036   0.148   1620
  Planarity :  0.002   0.025   1944
  Dihedral  : 13.204  82.606   4098
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.10 (0.23), residues: 1347
  helix:  1.00 (0.25), residues: 459
  sheet:  0.03 (0.31), residues: 282
  loop :  1.14 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 206 
 TYR   0.008   0.001   TYR A 417 
 PHE   0.007   0.001   PHE A 263 
 TRP   0.005   0.001   TRP C 233 
 HIS   0.001   0.000   HIS B 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00156 (11100)
  covalent geometry    : angle       0.45051 (15009)
  SS BOND              : bond        0.00166 (   21)
  SS BOND              : angle       0.70382 (   42)
  hydrogen bonds       : bond        0.21182 (  513)
  hydrogen bonds       : angle       8.74015 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ARG cc_start: 0.5864 (mtp85) cc_final: 0.5532 (mmm-85)
REVERT: A   51 LEU cc_start: 0.8158 (mm) cc_final: 0.7667 (pp)
REVERT: A   63 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8651 (tm-30)
REVERT: A   76 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8357 (tttm)
REVERT: A   80 VAL cc_start: 0.7610 (m) cc_final: 0.7338 (m)
REVERT: A  124 ILE cc_start: 0.8528 (mm) cc_final: 0.8311 (mm)
REVERT: A  129 MET cc_start: 0.8498 (tpp) cc_final: 0.7787 (tpp)
REVERT: A  133 LYS cc_start: 0.9035 (tppt) cc_final: 0.8636 (tppt)
REVERT: A  145 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8511 (ttm-80)
REVERT: A  168 MET cc_start: 0.8988 (ttp) cc_final: 0.8680 (ttp)
REVERT: A  362 VAL cc_start: 0.9299 (m) cc_final: 0.9032 (m)
REVERT: A  380 LYS cc_start: 0.8052 (tttp) cc_final: 0.7503 (tptp)
REVERT: B   51 LEU cc_start: 0.8086 (mm) cc_final: 0.7624 (pp)
REVERT: B   63 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8608 (tm-30)
REVERT: B   76 LYS cc_start: 0.8583 (ptmt) cc_final: 0.8256 (ptmm)
REVERT: B   78 ASP cc_start: 0.7984 (m-30) cc_final: 0.7745 (m-30)
REVERT: B  133 LYS cc_start: 0.9060 (tppt) cc_final: 0.8669 (tppt)
REVERT: B  145 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8481 (ttm-80)
REVERT: B  380 LYS cc_start: 0.8101 (tttp) cc_final: 0.7455 (tptm)
REVERT: C   43 ARG cc_start: 0.5926 (mtp85) cc_final: 0.5667 (mmm-85)
REVERT: C   51 LEU cc_start: 0.8189 (mm) cc_final: 0.7671 (pp)
REVERT: C   63 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8651 (tm-30)
REVERT: C   76 LYS cc_start: 0.8638 (ptmt) cc_final: 0.8373 (tttm)
REVERT: C   78 ASP cc_start: 0.8113 (m-30) cc_final: 0.7877 (m-30)
REVERT: C  129 MET cc_start: 0.8518 (tpp) cc_final: 0.7822 (tpp)
REVERT: C  133 LYS cc_start: 0.9038 (tppt) cc_final: 0.8677 (tppt)
REVERT: C  145 ARG cc_start: 0.8800 (mtm-85) cc_final: 0.8522 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.5727
  time to fit residues: 141.8031
Evaluate side-chains
  124 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.3980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 143 ASN
B  66 GLN
B 143 ASN
C  66 GLN
C 143 ASN
C 270 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.115829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.083021 restraints weight = 18332.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.95
r_work: 0.2946 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11121  Z= 0.144
  Angle     :  0.596   7.161  15051  Z= 0.303
  Chirality :  0.042   0.161   1620
  Planarity :  0.004   0.032   1944
  Dihedral  :  4.188  15.557   1476
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.90 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.04 (0.23), residues: 1347
  helix:  1.06 (0.24), residues: 498
  sheet: -0.14 (0.30), residues: 270
  loop :  1.04 (0.27), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 204 
 TYR   0.021   0.002   TYR A  71 
 PHE   0.011   0.001   PHE C 152 
 TRP   0.005   0.001   TRP B  46 
 HIS   0.003   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11100)
  covalent geometry    : angle       0.58874 (15009)
  SS BOND              : bond        0.00276 (   21)
  SS BOND              : angle       1.79696 (   42)
  hydrogen bonds       : bond        0.03869 (  513)
  hydrogen bonds       : angle       6.31123 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A   43 ARG cc_start: 0.5703 (mtp85) cc_final: 0.5323 (mmm-85)
REVERT: A   76 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7598 (tttm)
REVERT: A   78 ASP cc_start: 0.7701 (m-30) cc_final: 0.7366 (m-30)
REVERT: A  133 LYS cc_start: 0.8717 (tppt) cc_final: 0.8282 (tppt)
REVERT: A  139 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8343 (mt0)
REVERT: A  168 MET cc_start: 0.8625 (ttp) cc_final: 0.8421 (ttp)
REVERT: A  380 LYS cc_start: 0.7723 (tttp) cc_final: 0.7170 (tptp)
REVERT: B   43 ARG cc_start: 0.5931 (mtp85) cc_final: 0.5490 (mmm-85)
REVERT: B   63 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8708 (tm-30)
REVERT: B   76 LYS cc_start: 0.7757 (ptmt) cc_final: 0.7537 (ptmm)
REVERT: B   78 ASP cc_start: 0.7962 (m-30) cc_final: 0.7660 (m-30)
REVERT: B  133 LYS cc_start: 0.8728 (tppt) cc_final: 0.8307 (tppt)
REVERT: B  145 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8470 (mpp80)
REVERT: B  378 MET cc_start: 0.8486 (ptp) cc_final: 0.8195 (ptm)
REVERT: B  380 LYS cc_start: 0.7614 (tttp) cc_final: 0.6932 (tptm)
REVERT: C   43 ARG cc_start: 0.5612 (mtp85) cc_final: 0.5234 (mmm-85)
REVERT: C  129 MET cc_start: 0.8225 (tpp) cc_final: 0.7986 (tpp)
REVERT: C  133 LYS cc_start: 0.8666 (tppt) cc_final: 0.8219 (tppt)
REVERT: C  139 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8369 (mt0)
  outliers start: 17
  outliers final: 8
  residues processed: 155
  average time/residue: 0.5694
  time to fit residues: 95.1839
Evaluate side-chains
  120 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue  189 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 67 optimal weight:    0.0040
   chunk 109 optimal weight:    0.6980
   chunk 114 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
B  66 GLN
B  84 GLN
C  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.116182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.083083 restraints weight = 18339.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.92
r_work: 0.2924 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11121  Z= 0.134
  Angle     :  0.542   6.882  15051  Z= 0.276
  Chirality :  0.040   0.152   1620
  Planarity :  0.003   0.045   1944
  Dihedral  :  4.238  15.392   1476
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.76 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.11 (0.23), residues: 1347
  helix:  1.24 (0.24), residues: 507
  sheet: -0.05 (0.30), residues: 264
  loop :  0.90 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 204 
 TYR   0.029   0.002   TYR B 456 
 PHE   0.015   0.001   PHE B 442 
 TRP   0.011   0.001   TRP A  46 
 HIS   0.002   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11100)
  covalent geometry    : angle       0.53864 (15009)
  SS BOND              : bond        0.00453 (   21)
  SS BOND              : angle       1.25749 (   42)
  hydrogen bonds       : bond        0.03419 (  513)
  hydrogen bonds       : angle       5.78949 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   43 ARG cc_start: 0.5640 (mtp85) cc_final: 0.5239 (mmm-85)
REVERT: A   78 ASP cc_start: 0.7726 (m-30) cc_final: 0.7351 (m-30)
REVERT: A  104 SER cc_start: 0.8442 (t) cc_final: 0.8082 (p)
REVERT: A  129 MET cc_start: 0.8149 (tpp) cc_final: 0.7711 (tpp)
REVERT: A  133 LYS cc_start: 0.8704 (tppt) cc_final: 0.8263 (tppt)
REVERT: A  208 LYS cc_start: 0.8334 (mttt) cc_final: 0.8105 (mtpp)
REVERT: A  380 LYS cc_start: 0.7711 (tttp) cc_final: 0.7167 (tptp)
REVERT: B   43 ARG cc_start: 0.5859 (mtp85) cc_final: 0.5429 (mmm-85)
REVERT: B   63 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: B   76 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7544 (ptmm)
REVERT: B   78 ASP cc_start: 0.7967 (m-30) cc_final: 0.7686 (m-30)
REVERT: B  104 SER cc_start: 0.8391 (t) cc_final: 0.8109 (p)
REVERT: B  129 MET cc_start: 0.8299 (tpp) cc_final: 0.7890 (tpp)
REVERT: B  133 LYS cc_start: 0.8730 (tppt) cc_final: 0.8271 (tppt)
REVERT: B  378 MET cc_start: 0.8525 (ptp) cc_final: 0.8228 (ptm)
REVERT: B  380 LYS cc_start: 0.7671 (tttp) cc_final: 0.7040 (tptm)
REVERT: C   63 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8723 (tm-30)
REVERT: C  104 SER cc_start: 0.8315 (t) cc_final: 0.7864 (p)
REVERT: C  129 MET cc_start: 0.8267 (tpp) cc_final: 0.7998 (tpp)
REVERT: C  133 LYS cc_start: 0.8648 (tppt) cc_final: 0.8196 (tppt)
REVERT: C  365 MET cc_start: 0.8572 (mmm) cc_final: 0.8216 (mmm)
  outliers start: 15
  outliers final: 7
  residues processed: 143
  average time/residue: 0.5322
  time to fit residues: 82.0546
Evaluate side-chains
  112 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  376 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 416 ASN
B  66 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN
C  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.113357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.080809 restraints weight = 18141.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.90
r_work: 0.2940 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11121  Z= 0.172
  Angle     :  0.607  11.782  15051  Z= 0.308
  Chirality :  0.041   0.154   1620
  Planarity :  0.003   0.028   1944
  Dihedral  :  4.462  22.337   1476
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.03 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.10 (0.23), residues: 1347
  helix:  1.37 (0.24), residues: 507
  sheet: -0.13 (0.30), residues: 264
  loop :  0.80 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 204 
 TYR   0.032   0.002   TYR B 456 
 PHE   0.014   0.001   PHE B 442 
 TRP   0.014   0.001   TRP A  46 
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11100)
  covalent geometry    : angle       0.59446 (15009)
  SS BOND              : bond        0.00522 (   21)
  SS BOND              : angle       2.39708 (   42)
  hydrogen bonds       : bond        0.03305 (  513)
  hydrogen bonds       : angle       5.64626 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   43 ARG cc_start: 0.5634 (mtp85) cc_final: 0.5230 (mmm-85)
REVERT: A   78 ASP cc_start: 0.7674 (m-30) cc_final: 0.7376 (m-30)
REVERT: A  129 MET cc_start: 0.8198 (tpp) cc_final: 0.7740 (tpp)
REVERT: A  133 LYS cc_start: 0.8735 (tppt) cc_final: 0.8275 (tppt)
REVERT: A  166 ARG cc_start: 0.8279 (mpp80) cc_final: 0.7960 (mpp80)
REVERT: A  208 LYS cc_start: 0.8255 (mttt) cc_final: 0.8014 (mtpp)
REVERT: A  380 LYS cc_start: 0.7647 (tttp) cc_final: 0.7121 (tptp)
REVERT: A  452 GLU cc_start: 0.8027 (tt0) cc_final: 0.7784 (tm-30)
REVERT: A  456 TYR cc_start: 0.7856 (t80) cc_final: 0.7618 (t80)
REVERT: B   43 ARG cc_start: 0.5845 (mtp85) cc_final: 0.5395 (mmm-85)
REVERT: B   63 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8682 (tm-30)
REVERT: B   76 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7559 (ptmm)
REVERT: B   78 ASP cc_start: 0.7961 (m-30) cc_final: 0.7657 (m-30)
REVERT: B  133 LYS cc_start: 0.8725 (tppt) cc_final: 0.8294 (tppt)
REVERT: B  208 LYS cc_start: 0.8283 (mttt) cc_final: 0.8040 (mttp)
REVERT: B  380 LYS cc_start: 0.7587 (tttp) cc_final: 0.6990 (tptm)
REVERT: C   43 ARG cc_start: 0.6024 (mmm-85) cc_final: 0.5806 (mmm-85)
REVERT: C  129 MET cc_start: 0.8344 (tpp) cc_final: 0.8088 (tpp)
REVERT: C  133 LYS cc_start: 0.8715 (tppt) cc_final: 0.8257 (tppt)
REVERT: C  365 MET cc_start: 0.8542 (mmm) cc_final: 0.8210 (mmm)
  outliers start: 21
  outliers final: 13
  residues processed: 131
  average time/residue: 0.5776
  time to fit residues: 81.1873
Evaluate side-chains
  114 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  441 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 133 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A  84 GLN
B  66 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN
C  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084081 restraints weight = 18173.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.73
r_work: 0.2878 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11121  Z= 0.166
  Angle     :  0.584  10.737  15051  Z= 0.298
  Chirality :  0.041   0.151   1620
  Planarity :  0.003   0.024   1944
  Dihedral  :  4.473  24.356   1476
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.87 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.11 (0.24), residues: 1347
  helix:  1.44 (0.24), residues: 507
  sheet: -0.26 (0.30), residues: 264
  loop :  0.81 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 145 
 TYR   0.036   0.002   TYR C 456 
 PHE   0.038   0.001   PHE C  69 
 TRP   0.020   0.002   TRP B  46 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (11100)
  covalent geometry    : angle       0.57342 (15009)
  SS BOND              : bond        0.00509 (   21)
  SS BOND              : angle       2.15878 (   42)
  hydrogen bonds       : bond        0.03098 (  513)
  hydrogen bonds       : angle       5.55266 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   43 ARG cc_start: 0.5758 (mtp85) cc_final: 0.5550 (mmm-85)
REVERT: A   78 ASP cc_start: 0.8105 (m-30) cc_final: 0.7835 (m-30)
REVERT: A  129 MET cc_start: 0.8411 (tpp) cc_final: 0.7915 (tpp)
REVERT: A  133 LYS cc_start: 0.8815 (tppt) cc_final: 0.8377 (tppt)
REVERT: A  359 GLU cc_start: 0.8825 (pt0) cc_final: 0.8363 (pp20)
REVERT: A  380 LYS cc_start: 0.8265 (tttp) cc_final: 0.7792 (tptp)
REVERT: A  452 GLU cc_start: 0.8080 (tt0) cc_final: 0.7781 (tm-30)
REVERT: B   63 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8778 (tm-30)
REVERT: B   69 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7804 (m-80)
REVERT: B   76 LYS cc_start: 0.8327 (ptmt) cc_final: 0.8006 (ptmm)
REVERT: B   78 ASP cc_start: 0.8328 (m-30) cc_final: 0.8037 (m-30)
REVERT: B  129 MET cc_start: 0.8495 (tpp) cc_final: 0.8277 (tpp)
REVERT: B  133 LYS cc_start: 0.8837 (tppt) cc_final: 0.8422 (tppt)
REVERT: B  208 LYS cc_start: 0.8734 (mttt) cc_final: 0.8532 (mttp)
REVERT: B  359 GLU cc_start: 0.8871 (pt0) cc_final: 0.8321 (pp20)
REVERT: B  380 LYS cc_start: 0.8230 (tttp) cc_final: 0.7721 (tptm)
REVERT: B  409 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8521 (m-30)
REVERT: C   43 ARG cc_start: 0.6094 (mmm-85) cc_final: 0.5855 (mmm-85)
REVERT: C  129 MET cc_start: 0.8550 (tpp) cc_final: 0.8319 (tpp)
REVERT: C  133 LYS cc_start: 0.8801 (tppt) cc_final: 0.8373 (tppt)
REVERT: C  208 LYS cc_start: 0.8825 (mttt) cc_final: 0.8603 (mttp)
REVERT: C  359 GLU cc_start: 0.8978 (pt0) cc_final: 0.8389 (pp20)
REVERT: C  365 MET cc_start: 0.8834 (mmm) cc_final: 0.8628 (mmm)
  outliers start: 26
  outliers final: 11
  residues processed: 138
  average time/residue: 0.6287
  time to fit residues: 93.2516
Evaluate side-chains
  118 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  441 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
B  66 GLN
B  84 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN
C  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.111930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.079466 restraints weight = 18104.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.85
r_work: 0.2873 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11121  Z= 0.179
  Angle     :  0.588  10.778  15051  Z= 0.299
  Chirality :  0.041   0.149   1620
  Planarity :  0.003   0.026   1944
  Dihedral  :  4.490  22.496   1476
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 14.21 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.11 (0.24), residues: 1347
  helix:  1.48 (0.24), residues: 507
  sheet: -0.35 (0.30), residues: 264
  loop :  0.82 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  43 
 TYR   0.037   0.002   TYR A 456 
 PHE   0.015   0.001   PHE B 442 
 TRP   0.029   0.002   TRP B  46 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (11100)
  covalent geometry    : angle       0.57862 (15009)
  SS BOND              : bond        0.00514 (   21)
  SS BOND              : angle       2.04755 (   42)
  hydrogen bonds       : bond        0.03043 (  513)
  hydrogen bonds       : angle       5.44206 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ARG cc_start: 0.5645 (mtp85) cc_final: 0.5380 (mmm-85)
REVERT: A   78 ASP cc_start: 0.7807 (m-30) cc_final: 0.7505 (m-30)
REVERT: A  129 MET cc_start: 0.8280 (tpp) cc_final: 0.7792 (tpp)
REVERT: A  133 LYS cc_start: 0.8777 (tppt) cc_final: 0.8304 (tppt)
REVERT: A  166 ARG cc_start: 0.8479 (mpp80) cc_final: 0.8201 (mpp80)
REVERT: A  359 GLU cc_start: 0.8827 (pt0) cc_final: 0.8280 (pp20)
REVERT: A  380 LYS cc_start: 0.7796 (tttp) cc_final: 0.7324 (tptp)
REVERT: A  452 GLU cc_start: 0.8041 (tt0) cc_final: 0.7715 (tm-30)
REVERT: B   43 ARG cc_start: 0.6172 (mmm-85) cc_final: 0.5563 (ttm-80)
REVERT: B   63 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8684 (tm-30)
REVERT: B   69 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7787 (m-80)
REVERT: B   76 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7648 (ptmm)
REVERT: B   78 ASP cc_start: 0.8109 (m-30) cc_final: 0.7898 (m-30)
REVERT: B  129 MET cc_start: 0.8325 (tpp) cc_final: 0.8122 (tpp)
REVERT: B  133 LYS cc_start: 0.8800 (tppt) cc_final: 0.8343 (tppt)
REVERT: B  359 GLU cc_start: 0.8895 (pt0) cc_final: 0.8287 (pp20)
REVERT: B  378 MET cc_start: 0.8706 (ptp) cc_final: 0.8379 (mtm)
REVERT: B  380 LYS cc_start: 0.7850 (tttp) cc_final: 0.7315 (tptm)
REVERT: B  409 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8299 (m-30)
REVERT: B  452 GLU cc_start: 0.8118 (tt0) cc_final: 0.7808 (tm-30)
REVERT: C  129 MET cc_start: 0.8388 (tpp) cc_final: 0.8113 (tpp)
REVERT: C  133 LYS cc_start: 0.8744 (tppt) cc_final: 0.8272 (tppt)
REVERT: C  208 LYS cc_start: 0.8456 (mttt) cc_final: 0.8169 (mttp)
REVERT: C  359 GLU cc_start: 0.9009 (pt0) cc_final: 0.8368 (pp20)
REVERT: C  365 MET cc_start: 0.8692 (mmm) cc_final: 0.8461 (mmm)
REVERT: C  452 GLU cc_start: 0.8046 (tt0) cc_final: 0.7742 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 141
  average time/residue: 0.5530
  time to fit residues: 83.8912
Evaluate side-chains
  131 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  441 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 76 optimal weight:    0.0770
   chunk 127 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 106 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A  73 HIS
B  66 GLN
B 416 ASN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.077776 restraints weight = 18059.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.82
r_work: 0.2882 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11121  Z= 0.235
  Angle     :  0.623  10.540  15051  Z= 0.317
  Chirality :  0.042   0.150   1620
  Planarity :  0.003   0.033   1944
  Dihedral  :  4.667  23.255   1476
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.47 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.07 (0.24), residues: 1347
  helix:  1.50 (0.24), residues: 501
  sheet: -0.51 (0.30), residues: 264
  loop :  0.83 (0.28), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  43 
 TYR   0.036   0.002   TYR A 456 
 PHE   0.015   0.001   PHE B 442 
 TRP   0.019   0.002   TRP B  46 
 HIS   0.005   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 (11100)
  covalent geometry    : angle       0.61221 (15009)
  SS BOND              : bond        0.00605 (   21)
  SS BOND              : angle       2.27515 (   42)
  hydrogen bonds       : bond        0.03117 (  513)
  hydrogen bonds       : angle       5.47308 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ARG cc_start: 0.5642 (mtp85) cc_final: 0.5194 (mmm-85)
REVERT: A   78 ASP cc_start: 0.7912 (m-30) cc_final: 0.7579 (m-30)
REVERT: A  129 MET cc_start: 0.8325 (tpp) cc_final: 0.7810 (tpp)
REVERT: A  133 LYS cc_start: 0.8819 (tppt) cc_final: 0.8304 (tppt)
REVERT: A  166 ARG cc_start: 0.8534 (mpp80) cc_final: 0.8234 (mpp80)
REVERT: A  359 GLU cc_start: 0.8840 (pt0) cc_final: 0.8312 (pp20)
REVERT: A  380 LYS cc_start: 0.7832 (tttp) cc_final: 0.7316 (tptp)
REVERT: A  452 GLU cc_start: 0.8042 (tt0) cc_final: 0.7696 (tm-30)
REVERT: B   43 ARG cc_start: 0.6122 (mmm-85) cc_final: 0.5852 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8765 (tm-30)
REVERT: B   69 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7874 (m-80)
REVERT: B   76 LYS cc_start: 0.8068 (ptmt) cc_final: 0.7715 (ptmm)
REVERT: B   78 ASP cc_start: 0.8166 (m-30) cc_final: 0.7874 (m-30)
REVERT: B  133 LYS cc_start: 0.8825 (tppt) cc_final: 0.8328 (tppt)
REVERT: B  380 LYS cc_start: 0.7838 (tttp) cc_final: 0.7306 (tptm)
REVERT: B  452 GLU cc_start: 0.8112 (tt0) cc_final: 0.7752 (tm-30)
REVERT: C   43 ARG cc_start: 0.5844 (mmm-85) cc_final: 0.5372 (ttm-80)
REVERT: C  129 MET cc_start: 0.8481 (tpp) cc_final: 0.8185 (tpp)
REVERT: C  133 LYS cc_start: 0.8755 (tppt) cc_final: 0.8271 (tppt)
REVERT: C  208 LYS cc_start: 0.8388 (mttt) cc_final: 0.7995 (mttp)
REVERT: C  452 GLU cc_start: 0.8082 (tt0) cc_final: 0.7750 (tm-30)
  outliers start: 30
  outliers final: 16
  residues processed: 136
  average time/residue: 0.5927
  time to fit residues: 86.8818
Evaluate side-chains
  131 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   70 HIS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  441 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
B  66 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.110985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.078268 restraints weight = 17902.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.84
r_work: 0.2845 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11121  Z= 0.175
  Angle     :  0.588   9.308  15051  Z= 0.299
  Chirality :  0.041   0.153   1620
  Planarity :  0.003   0.033   1944
  Dihedral  :  4.602  24.267   1476
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.23 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.27 (0.24), residues: 1347
  helix:  1.72 (0.24), residues: 489
  sheet: -0.34 (0.30), residues: 273
  loop :  0.90 (0.28), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 145 
 TYR   0.041   0.002   TYR A 456 
 PHE   0.015   0.001   PHE B 442 
 TRP   0.017   0.002   TRP B  46 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11100)
  covalent geometry    : angle       0.57931 (15009)
  SS BOND              : bond        0.00480 (   21)
  SS BOND              : angle       1.98180 (   42)
  hydrogen bonds       : bond        0.03006 (  513)
  hydrogen bonds       : angle       5.41577 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ARG cc_start: 0.5612 (mtp85) cc_final: 0.5186 (mmm-85)
REVERT: A   69 PHE cc_start: 0.8770 (m-80) cc_final: 0.8547 (m-80)
REVERT: A   78 ASP cc_start: 0.7923 (m-30) cc_final: 0.7607 (m-30)
REVERT: A  129 MET cc_start: 0.8304 (tpp) cc_final: 0.7839 (tpp)
REVERT: A  133 LYS cc_start: 0.8817 (tppt) cc_final: 0.8307 (tppt)
REVERT: A  166 ARG cc_start: 0.8555 (mpp80) cc_final: 0.8238 (mpp80)
REVERT: A  359 GLU cc_start: 0.8798 (pt0) cc_final: 0.8211 (pp20)
REVERT: A  380 LYS cc_start: 0.7772 (tttp) cc_final: 0.7289 (tptp)
REVERT: A  452 GLU cc_start: 0.8020 (tt0) cc_final: 0.7648 (tm-30)
REVERT: B   43 ARG cc_start: 0.6131 (mmm-85) cc_final: 0.5884 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8800 (tm-30)
REVERT: B   69 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7884 (m-80)
REVERT: B   76 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7660 (ptmm)
REVERT: B   78 ASP cc_start: 0.8225 (m-30) cc_final: 0.7931 (m-30)
REVERT: B  133 LYS cc_start: 0.8811 (tppt) cc_final: 0.8309 (tppt)
REVERT: B  189 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8749 (p)
REVERT: B  378 MET cc_start: 0.8708 (ptp) cc_final: 0.8383 (mtm)
REVERT: B  380 LYS cc_start: 0.7810 (tttp) cc_final: 0.7298 (tptm)
REVERT: B  452 GLU cc_start: 0.8123 (tt0) cc_final: 0.7737 (tm-30)
REVERT: C   43 ARG cc_start: 0.5797 (mmm-85) cc_final: 0.5389 (ttm-80)
REVERT: C  129 MET cc_start: 0.8451 (tpp) cc_final: 0.8136 (tpp)
REVERT: C  133 LYS cc_start: 0.8733 (tppt) cc_final: 0.8223 (tppt)
REVERT: C  189 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8872 (p)
REVERT: C  452 GLU cc_start: 0.8084 (tt0) cc_final: 0.7723 (tm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 145
  average time/residue: 0.5391
  time to fit residues: 84.7325
Evaluate side-chains
  134 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   70 HIS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  441 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 123 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 112 optimal weight:    0.3980
   chunk 115 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
B  66 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.112106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.079496 restraints weight = 17984.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.85
r_work: 0.2873 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11121  Z= 0.144
  Angle     :  0.573   8.914  15051  Z= 0.290
  Chirality :  0.040   0.150   1620
  Planarity :  0.003   0.033   1944
  Dihedral  :  4.535  24.332   1476
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.99 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.28 (0.24), residues: 1347
  helix:  1.81 (0.24), residues: 489
  sheet: -0.37 (0.30), residues: 276
  loop :  0.85 (0.28), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 145 
 TYR   0.040   0.002   TYR C 456 
 PHE   0.011   0.001   PHE B 442 
 TRP   0.016   0.002   TRP B  46 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11100)
  covalent geometry    : angle       0.56622 (15009)
  SS BOND              : bond        0.00440 (   21)
  SS BOND              : angle       1.79507 (   42)
  hydrogen bonds       : bond        0.02901 (  513)
  hydrogen bonds       : angle       5.33312 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ARG cc_start: 0.5584 (mtp85) cc_final: 0.5178 (mmm-85)
REVERT: A   69 PHE cc_start: 0.8780 (m-80) cc_final: 0.8494 (m-80)
REVERT: A   78 ASP cc_start: 0.7915 (m-30) cc_final: 0.7605 (m-30)
REVERT: A  104 SER cc_start: 0.8499 (t) cc_final: 0.8152 (p)
REVERT: A  129 MET cc_start: 0.8317 (tpp) cc_final: 0.7930 (tpp)
REVERT: A  133 LYS cc_start: 0.8785 (tppt) cc_final: 0.8266 (tppt)
REVERT: A  210 MET cc_start: 0.8268 (mpm) cc_final: 0.7789 (mpp)
REVERT: A  358 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8717 (tp40)
REVERT: A  359 GLU cc_start: 0.8709 (pt0) cc_final: 0.8137 (pp20)
REVERT: A  380 LYS cc_start: 0.7734 (tttp) cc_final: 0.7243 (tptp)
REVERT: A  452 GLU cc_start: 0.8022 (tt0) cc_final: 0.7636 (tm-30)
REVERT: B   43 ARG cc_start: 0.6102 (mmm-85) cc_final: 0.5886 (mmm-85)
REVERT: B   63 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: B   69 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7859 (m-80)
REVERT: B   76 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7648 (ptmm)
REVERT: B   78 ASP cc_start: 0.8173 (m-30) cc_final: 0.7880 (m-30)
REVERT: B  133 LYS cc_start: 0.8810 (tppt) cc_final: 0.8292 (tppt)
REVERT: B  189 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8740 (p)
REVERT: B  221 MET cc_start: 0.8636 (ttp) cc_final: 0.8421 (ttp)
REVERT: B  359 GLU cc_start: 0.8821 (pt0) cc_final: 0.8183 (pp20)
REVERT: B  378 MET cc_start: 0.8658 (ptp) cc_final: 0.8344 (mtm)
REVERT: B  380 LYS cc_start: 0.7704 (tttp) cc_final: 0.7186 (tptm)
REVERT: B  452 GLU cc_start: 0.8123 (tt0) cc_final: 0.7749 (tm-30)
REVERT: C   43 ARG cc_start: 0.5740 (mmm-85) cc_final: 0.5331 (ttm-80)
REVERT: C  129 MET cc_start: 0.8447 (tpp) cc_final: 0.8112 (tpp)
REVERT: C  133 LYS cc_start: 0.8717 (tppt) cc_final: 0.8202 (tppt)
REVERT: C  148 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8862 (mmmm)
REVERT: C  189 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8846 (p)
REVERT: C  359 GLU cc_start: 0.8956 (pt0) cc_final: 0.8279 (pp20)
REVERT: C  452 GLU cc_start: 0.8066 (tt0) cc_final: 0.7706 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 141
  average time/residue: 0.6452
  time to fit residues: 97.5033
Evaluate side-chains
  141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  358 GLN
Chi-restraints excluded: chain A residue  364 GLU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   70 HIS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  453 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 358 GLN
A 416 ASN
B  66 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.110251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.077484 restraints weight = 17973.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.85
r_work: 0.2828 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11121  Z= 0.209
  Angle     :  0.610   8.996  15051  Z= 0.308
  Chirality :  0.042   0.152   1620
  Planarity :  0.003   0.033   1944
  Dihedral  :  4.629  24.641   1476
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.99 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.16 (0.24), residues: 1347
  helix:  1.57 (0.24), residues: 507
  sheet: -0.45 (0.30), residues: 258
  loop :  0.86 (0.28), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 145 
 TYR   0.040   0.002   TYR B 456 
 PHE   0.013   0.001   PHE A 442 
 TRP   0.032   0.002   TRP A  46 
 HIS   0.003   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (11100)
  covalent geometry    : angle       0.60094 (15009)
  SS BOND              : bond        0.00533 (   21)
  SS BOND              : angle       2.06026 (   42)
  hydrogen bonds       : bond        0.02968 (  513)
  hydrogen bonds       : angle       5.35924 ( 1530)

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

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

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2694 Ramachandran restraints generated.
    1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ARG cc_start: 0.5554 (mtp85) cc_final: 0.5152 (mmm-85)
REVERT: A   78 ASP cc_start: 0.7931 (m-30) cc_final: 0.7627 (m-30)
REVERT: A  129 MET cc_start: 0.8360 (tpp) cc_final: 0.7967 (tpp)
REVERT: A  133 LYS cc_start: 0.8814 (tppt) cc_final: 0.8287 (tppt)
REVERT: A  210 MET cc_start: 0.8313 (mpm) cc_final: 0.7808 (mpp)
REVERT: A  358 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8647 (mm-40)
REVERT: A  359 GLU cc_start: 0.8743 (pt0) cc_final: 0.8222 (pp20)
REVERT: A  380 LYS cc_start: 0.7722 (tttp) cc_final: 0.7247 (tptp)
REVERT: A  452 GLU cc_start: 0.8035 (tt0) cc_final: 0.7663 (tm-30)
REVERT: B   43 ARG cc_start: 0.6162 (mmm-85) cc_final: 0.5947 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8794 (tm-30)
REVERT: B   69 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7919 (m-80)
REVERT: B   76 LYS cc_start: 0.8034 (ptmt) cc_final: 0.7649 (ptmm)
REVERT: B   78 ASP cc_start: 0.8198 (m-30) cc_final: 0.7879 (m-30)
REVERT: B  133 LYS cc_start: 0.8833 (tppt) cc_final: 0.8305 (tppt)
REVERT: B  359 GLU cc_start: 0.8837 (pt0) cc_final: 0.8251 (pp20)
REVERT: B  378 MET cc_start: 0.8676 (ptp) cc_final: 0.8346 (mtm)
REVERT: B  380 LYS cc_start: 0.7797 (tttp) cc_final: 0.7279 (tptm)
REVERT: B  452 GLU cc_start: 0.8119 (tt0) cc_final: 0.7739 (tm-30)
REVERT: C   43 ARG cc_start: 0.5770 (mmm-85) cc_final: 0.5404 (ttt90)
REVERT: C  129 MET cc_start: 0.8500 (tpp) cc_final: 0.8129 (tpp)
REVERT: C  133 LYS cc_start: 0.8748 (tppt) cc_final: 0.8217 (tppt)
REVERT: C  148 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8821 (mmmm)
REVERT: C  359 GLU cc_start: 0.8995 (pt0) cc_final: 0.8310 (pp20)
REVERT: C  452 GLU cc_start: 0.8083 (tt0) cc_final: 0.7739 (tm-30)
  outliers start: 25
  outliers final: 19
  residues processed: 135
  average time/residue: 0.6323
  time to fit residues: 91.9961
Evaluate side-chains
  141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  358 GLN
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   70 HIS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  148 LYS
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  453 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 120 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 128 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 131 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
A  66 GLN
B  66 GLN
** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 GLN
** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.111179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.078586 restraints weight = 17963.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.84
r_work: 0.2855 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11121  Z= 0.161
  Angle     :  0.593   9.276  15051  Z= 0.299
  Chirality :  0.041   0.149   1620
  Planarity :  0.003   0.033   1944
  Dihedral  :  4.600  25.355   1476
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.41 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 are not related in a simple way.
  whole:  1.18 (0.24), residues: 1347
  helix:  1.63 (0.24), residues: 504
  sheet: -0.46 (0.30), residues: 258
  loop :  0.83 (0.28), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 201 
 TYR   0.043   0.002   TYR A 456 
 PHE   0.011   0.001   PHE C 263 
 TRP   0.085   0.004   TRP A  46 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11100)
  covalent geometry    : angle       0.58519 (15009)
  SS BOND              : bond        0.00457 (   21)
  SS BOND              : angle       1.86471 (   42)
  hydrogen bonds       : bond        0.02925 (  513)
  hydrogen bonds       : angle       5.29338 ( 1530)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3679.52 seconds
wall clock time: 63 minutes 32.49 seconds (3812.49 seconds total)