Starting phenix.real_space_refine
on Sun Oct 25 00:57:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9y6p_72626/10_2026/9y6p_72626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9y6p_72626/10_2026/9y6p_72626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9y6p_72626/10_2026/9y6p_72626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9y6p_72626/10_2026/9y6p_72626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9y6p_72626/10_2026/9y6p_72626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9y6p_72626/10_2026/9y6p_72626.cif"
  }
  resolution = 3.88
  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=   0.006 sd=   0.038
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: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      96      5.16       5
     C    9704      2.51       5
     N    2336      2.21       5
     O    2676      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14824
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3659
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 6, 'TRANS': 441}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 47
          Unusual residues: {'EUJ': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.49, per 1000 atoms: 0.24
  Number of scatterers: 14824
  At special positions: 0
  Unit cell: (101.755, 101.755, 117.992, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      96     16.00
     P      12     15.00
     O    2676      8.00
     N    2336      7.00
     C    9704      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 243 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 164 " - pdb=" SG  CYS C 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 243 " - pdb=" SG  CYS C 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 164 " - pdb=" SG  CYS B 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 243 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 164 " - pdb=" SG  CYS D 190 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 243 " - pdb=" SG  CYS D 274 " 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: 1.16
  Conformation dependent library (CDL) restraints added in 631.4 milliseconds
  

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3424

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 4 sheets defined
      68.6% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 50
      removed outlier: 4.354A  pdb=" N   GLU A  43 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASP A  44 " --> pdb=" O   CYS A  40 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   TYR A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 65 through 106
      removed outlier: 3.545A  pdb=" N   LEU A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 140
    Processing helix  chain 'A' and resid 140 through 145
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 3.869A  pdb=" N   SER A 237 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 329
    Processing helix  chain 'A' and resid 336 through 341
    Processing helix  chain 'A' and resid 344 through 371
    Processing helix  chain 'A' and resid 376 through 398
      removed outlier: 4.185A  pdb=" N   ILE A 394 " --> pdb=" O   TRP A 390 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TYR A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 443
      Proline residue:  A 415  - end of helix
      removed outlier: 3.804A  pdb=" N   ARG A 419 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   PHE A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      Proline residue:  A 441  - end of helix
    Processing helix  chain 'A' and resid 448 through 462
    Processing helix  chain 'A' and resid 464 through 471
    Processing helix  chain 'A' and resid 476 through 515
    Processing helix  chain 'C' and resid 40 through 50
      removed outlier: 4.108A  pdb=" N   ASP C  44 " --> pdb=" O   CYS C  40 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS C  46 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   TYR C  48 " --> pdb=" O   ASP C  44 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE C  49 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 59
    Processing helix  chain 'C' and resid 65 through 106
      removed outlier: 3.545A  pdb=" N   LEU C 106 " --> pdb=" O   LYS C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 140
    Processing helix  chain 'C' and resid 140 through 145
    Processing helix  chain 'C' and resid 194 through 199
    Processing helix  chain 'C' and resid 208 through 212
    Processing helix  chain 'C' and resid 214 through 216
      No H-bonds generated for 'chain 'C' and resid 214 through 216'
    Processing helix  chain 'C' and resid 232 through 238
      removed outlier: 3.869A  pdb=" N   SER C 237 " --> pdb=" O   GLN C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 329
    Processing helix  chain 'C' and resid 336 through 341
    Processing helix  chain 'C' and resid 344 through 371
    Processing helix  chain 'C' and resid 376 through 398
      removed outlier: 4.185A  pdb=" N   ILE C 394 " --> pdb=" O   TRP C 390 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG C 395 " --> pdb=" O   VAL C 391 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TYR C 396 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 400 through 443
      Proline residue:  C 415  - end of helix
      removed outlier: 3.804A  pdb=" N   ARG C 419 " --> pdb=" O   PRO C 415 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   PHE C 420 " --> pdb=" O   LYS C 416 " (cutoff:3.500A)
      Proline residue:  C 441  - end of helix
    Processing helix  chain 'C' and resid 448 through 462
    Processing helix  chain 'C' and resid 464 through 471
    Processing helix  chain 'C' and resid 476 through 515
    Processing helix  chain 'B' and resid 40 through 50
      removed outlier: 4.109A  pdb=" N   ASP B  44 " --> pdb=" O   CYS B  40 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS B  46 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   TYR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
    Processing helix  chain 'B' and resid 65 through 106
      removed outlier: 3.545A  pdb=" N   LEU B 106 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 140
    Processing helix  chain 'B' and resid 140 through 145
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 208 through 212
    Processing helix  chain 'B' and resid 214 through 216
      No H-bonds generated for 'chain 'B' and resid 214 through 216'
    Processing helix  chain 'B' and resid 232 through 238
      removed outlier: 3.868A  pdb=" N   SER B 237 " --> pdb=" O   GLN B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 329
    Processing helix  chain 'B' and resid 336 through 341
    Processing helix  chain 'B' and resid 344 through 371
    Processing helix  chain 'B' and resid 376 through 398
      removed outlier: 4.185A  pdb=" N   ILE B 394 " --> pdb=" O   TRP B 390 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG B 395 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TYR B 396 " --> pdb=" O   GLY B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 443
      Proline residue:  B 415  - end of helix
      removed outlier: 3.804A  pdb=" N   ARG B 419 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   PHE B 420 " --> pdb=" O   LYS B 416 " (cutoff:3.500A)
      Proline residue:  B 441  - end of helix
    Processing helix  chain 'B' and resid 448 through 462
    Processing helix  chain 'B' and resid 464 through 471
    Processing helix  chain 'B' and resid 476 through 515
    Processing helix  chain 'D' and resid 40 through 50
      removed outlier: 4.108A  pdb=" N   ASP D  44 " --> pdb=" O   CYS D  40 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS D  46 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   TYR D  48 " --> pdb=" O   ASP D  44 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE D  49 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 59
    Processing helix  chain 'D' and resid 65 through 106
      removed outlier: 3.544A  pdb=" N   LEU D 106 " --> pdb=" O   LYS D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 140
    Processing helix  chain 'D' and resid 140 through 145
    Processing helix  chain 'D' and resid 194 through 199
    Processing helix  chain 'D' and resid 208 through 212
    Processing helix  chain 'D' and resid 214 through 216
      No H-bonds generated for 'chain 'D' and resid 214 through 216'
    Processing helix  chain 'D' and resid 232 through 238
      removed outlier: 3.869A  pdb=" N   SER D 237 " --> pdb=" O   GLN D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 329
    Processing helix  chain 'D' and resid 336 through 341
    Processing helix  chain 'D' and resid 344 through 371
    Processing helix  chain 'D' and resid 376 through 398
      removed outlier: 4.185A  pdb=" N   ILE D 394 " --> pdb=" O   TRP D 390 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ARG D 395 " --> pdb=" O   VAL D 391 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TYR D 396 " --> pdb=" O   GLY D 392 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 400 through 443
      Proline residue:  D 415  - end of helix
      removed outlier: 3.803A  pdb=" N   ARG D 419 " --> pdb=" O   PRO D 415 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   PHE D 420 " --> pdb=" O   LYS D 416 " (cutoff:3.500A)
      Proline residue:  D 441  - end of helix
    Processing helix  chain 'D' and resid 448 through 462
    Processing helix  chain 'D' and resid 464 through 471
    Processing helix  chain 'D' and resid 476 through 515
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 119 through 121
    current: chain 'A' and resid 186 through 187
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 186 through 187
    current: chain 'A' and resid 243 through 253
    Processing sheet with id=AA2, first strand: chain 'C' and resid 119 through 121
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 119 through 121
    current: chain 'C' and resid 186 through 187
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 186 through 187
    current: chain 'C' and resid 243 through 253
    Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 119 through 121
    current: chain 'B' and resid 186 through 187
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 186 through 187
    current: chain 'B' and resid 243 through 253
    Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 119 through 121
    current: chain 'D' and resid 186 through 187
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 186 through 187
    current: chain 'D' and resid 243 through 253

    904 hydrogen bonds defined for protein.
    2688 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2501
        1.33 -     1.45: 4090
        1.45 -     1.57: 8385
        1.57 -     1.70: 36
        1.70 -     1.82: 132
  Bond restraints: 15144
  Sorted by residual:
  bond pdb=" O3  EUJ D 601 "
       pdb=" P3  EUJ D 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.611  0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" O3  EUJ A 601 "
       pdb=" P3  EUJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.611  0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" O3  EUJ C 601 "
       pdb=" P3  EUJ C 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.611  0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" O3  EUJ B 601 "
       pdb=" P3  EUJ B 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.612  0.115 2.00e-02 2.50e+03 3.33e+01
  bond pdb=" O12 EUJ A 601 "
       pdb=" P1  EUJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.606 -0.109 2.00e-02 2.50e+03 2.95e+01
  ... (remaining 15139 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 20173
        2.49 -     4.98: 222
        4.98 -     7.47: 63
        7.47 -     9.96: 6
        9.96 -    12.45: 24
  Bond angle restraints: 20488
  Sorted by residual:
  angle pdb=" O11 EUJ B 601 "
        pdb=" P1  EUJ B 601 "
        pdb=" O12 EUJ B 601 "
      ideal   model   delta    sigma   weight residual
     121.88  109.43   12.45 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" O11 EUJ C 601 "
        pdb=" P1  EUJ C 601 "
        pdb=" O12 EUJ C 601 "
      ideal   model   delta    sigma   weight residual
     121.88  109.43   12.45 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" O11 EUJ A 601 "
        pdb=" P1  EUJ A 601 "
        pdb=" O12 EUJ A 601 "
      ideal   model   delta    sigma   weight residual
     121.88  109.46   12.42 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" O11 EUJ D 601 "
        pdb=" P1  EUJ D 601 "
        pdb=" O12 EUJ D 601 "
      ideal   model   delta    sigma   weight residual
     121.88  109.46   12.42 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" CA  PRO C 202 "
        pdb=" N   PRO C 202 "
        pdb=" CD  PRO C 202 "
      ideal   model   delta    sigma   weight residual
     112.00  106.30    5.70 1.40e+00 5.10e-01 1.66e+01
  ... (remaining 20483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 8758
       35.96 -    71.93: 278
       71.93 -   107.89: 20
      107.89 -   143.86: 20
      143.86 -   179.82: 4
  Dihedral angle restraints: 9080
    sinusoidal: 3788
      harmonic: 5292
  Sorted by residual:
  dihedral pdb=" C1  EUJ A 601 "
           pdb=" O1  EUJ A 601 "
           pdb=" P1  EUJ A 601 "
           pdb=" O13 EUJ A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.32  118.50 -179.82     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C1  EUJ D 601 "
           pdb=" O1  EUJ D 601 "
           pdb=" P1  EUJ D 601 "
           pdb=" O13 EUJ D 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.32  118.49 -179.81     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C1  EUJ C 601 "
           pdb=" O1  EUJ C 601 "
           pdb=" P1  EUJ C 601 "
           pdb=" O13 EUJ C 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.32  118.48 -179.80     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 9077 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.972: 2356
       0.972 -    1.944: 0
       1.944 -    2.916: 0
       2.916 -    3.888: 0
       3.888 -    4.860: 4
  Chirality restraints: 2360
  Sorted by residual:
  chirality pdb=" C1  EUJ C 601 "
            pdb=" C2  EUJ C 601 "
            pdb=" C6  EUJ C 601 "
            pdb=" O1  EUJ C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41   -2.45    4.86 2.00e-01 2.50e+01 5.91e+02
  chirality pdb=" C1  EUJ D 601 "
            pdb=" C2  EUJ D 601 "
            pdb=" C6  EUJ D 601 "
            pdb=" O1  EUJ D 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41   -2.45    4.86 2.00e-01 2.50e+01 5.91e+02
  chirality pdb=" C1  EUJ A 601 "
            pdb=" C2  EUJ A 601 "
            pdb=" C6  EUJ A 601 "
            pdb=" O1  EUJ A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41   -2.45    4.86 2.00e-01 2.50e+01 5.90e+02
  ... (remaining 2357 not shown)

  Planarity restraints: 2480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 201 "    0.081 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO D 202 "   -0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO D 202 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO D 202 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 201 "   -0.080 5.00e-02 4.00e+02   1.19e-01 2.27e+01
        pdb=" N   PRO A 202 "    0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO A 202 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 202 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 201 "   -0.080 5.00e-02 4.00e+02   1.19e-01 2.27e+01
        pdb=" N   PRO B 202 "    0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO B 202 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO B 202 "   -0.064 5.00e-02 4.00e+02
  ... (remaining 2477 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 268
        2.69 -     3.25: 15005
        3.25 -     3.80: 24037
        3.80 -     4.35: 28571
        4.35 -     4.90: 48517
  Nonbonded interactions: 116398
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 428 "
            pdb=" O   ALA C 453 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OH  TYR B 428 "
            pdb=" O   ALA B 453 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OH  TYR A 428 "
            pdb=" O   ALA A 453 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OH  TYR D 428 "
            pdb=" O   ALA D 453 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   ASP C 204 "
            pdb=" OG1 THR C 208 "
     model   vdw
     2.230 3.040
  ... (remaining 116393 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     13.760
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4287
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116  15152  Z= 0.262
  Angle     :  0.769  12.455  20504  Z= 0.354
  Chirality :  0.205   4.860   2360
  Planarity :  0.006   0.119   2480
  Dihedral  : 18.546 179.824   5632
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  0.49 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.20), residues: 1760
  helix:  2.40 (0.15), residues: 1084
  sheet: -1.73 (0.44), residues: 152
  loop : -0.28 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  57 
 TYR   0.011   0.001   TYR B  48 
 PHE   0.016   0.001   PHE B 388 
 TRP   0.010   0.001   TRP C  64 
 HIS   0.002   0.001   HIS C 443 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00526 /  0.26 (15144)
  covalent geometry    : angle       0.76845 /  0.35 (20488)
  SS BOND              : bond        0.00527 /  0.29 (    8)
  SS BOND              : angle       1.16712 /  0.63 (   16)
  hydrogen bonds       : bond        0.10351 /  7.24 (  904)
  hydrogen bonds       : angle       5.28570 /  3.98 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 369
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7496 (mtmm) cc_final: 0.6776 (mmtt)
REVERT: A   75 MET cc_start: 0.6408 (mmp) cc_final: 0.5910 (mmt)
REVERT: A  141 LEU cc_start: 0.7478 (tp) cc_final: 0.7123 (tp)
REVERT: A  293 PHE cc_start: 0.4737 (t80) cc_final: 0.4219 (t80)
REVERT: A  370 LYS cc_start: 0.6644 (mmtt) cc_final: 0.6238 (mmtm)
REVERT: A  419 ARG cc_start: 0.6455 (mtm180) cc_final: 0.4986 (ptt90)
REVERT: A  426 MET cc_start: 0.7127 (mmm) cc_final: 0.6628 (mmm)
REVERT: C  358 ILE cc_start: 0.5807 (mm) cc_final: 0.5435 (mm)
REVERT: B   65 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4918 (mmtm)
REVERT: B  409 THR cc_start: 0.7606 (p) cc_final: 0.7381 (p)
REVERT: B  510 TYR cc_start: 0.7276 (t80) cc_final: 0.4602 (m-10)
  outliers start: 8
  outliers final: 2
  residues processed: 374
  average time/residue: 0.1120
  time to fit residues: 62.2642
Evaluate side-chains
  234 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 231
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain D residue   55 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149]
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 339 GLN
C 248 ASN
C 254 ASN
B 220 GLN
D 143 ASN
D 196 GLN
D 220 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.220609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 108)---------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.184904 restraints weight = 19524.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.184948 restraints weight = 17079.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.184948 restraints weight = 16806.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.184948 restraints weight = 16806.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.184948 restraints weight = 16806.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.8486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  15152  Z= 0.285
  Angle     :  0.860  12.307  20504  Z= 0.439
  Chirality :  0.047   0.246   2360
  Planarity :  0.005   0.072   2480
  Dihedral  : 14.553 123.027   2220
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 13.76 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.20), residues: 1760
  helix:  1.73 (0.15), residues: 1080
  sheet: -2.00 (0.42), residues: 144
  loop : -0.37 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  82 
 TYR   0.029   0.003   TYR A 428 
 PHE   0.034   0.003   PHE A 109 
 TRP   0.014   0.002   TRP A 436 
 HIS   0.006   0.002   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00630 /  0.28 (15144)
  covalent geometry    : angle       0.85676 /  0.44 (20488)
  SS BOND              : bond        0.02515 /  1.23 (    8)
  SS BOND              : angle       2.82423 /  1.57 (   16)
  hydrogen bonds       : bond        0.06201 /  4.00 (  904)
  hydrogen bonds       : angle       4.78354 /  3.39 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 292
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7555 (mtmm) cc_final: 0.6830 (mmtt)
REVERT: A   83 PHE cc_start: 0.7793 (t80) cc_final: 0.7538 (t80)
REVERT: A  370 LYS cc_start: 0.6792 (mmtt) cc_final: 0.6515 (mmtt)
REVERT: A  397 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: C  151 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5430 (m-80)
REVERT: C  356 MET cc_start: 0.7414 (tpp) cc_final: 0.7204 (mmt)
REVERT: C  365 MET cc_start: 0.7292 (tpt) cc_final: 0.6874 (tpt)
REVERT: C  497 MET cc_start: 0.5939 (mtt) cc_final: 0.5593 (mtt)
REVERT: D  191 ILE cc_start: 0.4903 (pt) cc_final: 0.4684 (pt)
REVERT: D  298 ILE cc_start: 0.6456 (mm) cc_final: 0.6182 (mm)
REVERT: D  365 MET cc_start: 0.8288 (mmm) cc_final: 0.8041 (mmm)
  outliers start: 43
  outliers final: 21
  residues processed: 322
  average time/residue: 0.1064
  time to fit residues: 52.1423
Evaluate side-chains
  240 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 217
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  151 TYR
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  340 TRP
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  192 HIS
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  348 VAL
Chi-restraints excluded: chain D residue  352 ILE
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain D residue  427 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  472 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [108, 139, 92, 104, 162, 44, 21, 51, 132, 55, 126]
   chunk 108 optimal weight:    1.9990
   chunk 139 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9980
   chunk 162 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 132 optimal weight:   20.0000
   chunk 55 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 339 GLN
C 443 HIS
B 471 GLN
D 143 ASN
D 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.218457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180706 restraints weight = 19419.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.181181 restraints weight = 15750.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.181224 restraints weight = 13608.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.181236 restraints weight = 12911.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.181286 restraints weight = 12743.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.9808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15152  Z= 0.160
  Angle     :  0.579  10.146  20504  Z= 0.302
  Chirality :  0.040   0.166   2360
  Planarity :  0.004   0.065   2480
  Dihedral  : 12.860 154.642   2208
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.92 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.20), residues: 1760
  helix:  2.45 (0.15), residues: 1068
  sheet: -1.97 (0.40), residues: 152
  loop : -0.13 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  82 
 TYR   0.019   0.002   TYR B 486 
 PHE   0.034   0.002   PHE A 109 
 TRP   0.018   0.001   TRP D 390 
 HIS   0.008   0.001   HIS B 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 (15144)
  covalent geometry    : angle       0.57719 /  0.30 (20488)
  SS BOND              : bond        0.00944 /  0.60 (    8)
  SS BOND              : angle       1.73485 /  0.98 (   16)
  hydrogen bonds       : bond        0.04662 /  3.01 (  904)
  hydrogen bonds       : angle       4.09685 /  2.94 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 254
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7557 (mtmm) cc_final: 0.6917 (mmtt)
REVERT: A   83 PHE cc_start: 0.7850 (t80) cc_final: 0.7622 (t80)
REVERT: A  249 THR cc_start: 0.9038 (p) cc_final: 0.8711 (p)
REVERT: A  370 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6890 (mmtt)
REVERT: A  436 TRP cc_start: 0.8632 (t60) cc_final: 0.8374 (t60)
REVERT: A  448 ASN cc_start: 0.7276 (m110) cc_final: 0.6902 (t0)
REVERT: C  418 LEU cc_start: 0.8646 (tp) cc_final: 0.8369 (tt)
REVERT: C  426 MET cc_start: 0.8621 (tpp) cc_final: 0.8398 (tpp)
REVERT: D   96 ASP cc_start: 0.8298 (t70) cc_final: 0.7677 (t70)
REVERT: D  191 ILE cc_start: 0.5174 (pt) cc_final: 0.4898 (pt)
  outliers start: 34
  outliers final: 19
  residues processed: 280
  average time/residue: 0.0946
  time to fit residues: 42.3285
Evaluate side-chains
  229 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 210
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  386 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  192 HIS
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  418 LEU
Chi-restraints excluded: chain D residue  427 ILE
Chi-restraints excluded: chain D residue  479 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [8, 12, 25, 127, 160, 69, 15, 103, 51, 94, 66]
   chunk 8 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 127 optimal weight:    2.9990
   chunk 160 optimal weight:    0.9990
   chunk 69 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0050
   chunk 94 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    0.8600

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 339 GLN
C 192 HIS
C 461 ASN
D 143 ASN
D 196 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.216874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.179408 restraints weight = 19466.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.180146 restraints weight = 15908.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.179823 restraints weight = 14174.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.179880 restraints weight = 15012.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.179966 restraints weight = 13416.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          1.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15152  Z= 0.136
  Angle     :  0.550  11.301  20504  Z= 0.286
  Chirality :  0.039   0.176   2360
  Planarity :  0.004   0.055   2480
  Dihedral  : 12.647 179.185   2208
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.93 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.20), residues: 1760
  helix:  2.62 (0.15), residues: 1068
  sheet: -1.94 (0.41), residues: 156
  loop : -0.04 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 310 
 TYR   0.019   0.001   TYR A 486 
 PHE   0.030   0.002   PHE A 109 
 TRP   0.015   0.001   TRP D 205 
 HIS   0.005   0.001   HIS B 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.14 (15144)
  covalent geometry    : angle       0.54836 /  0.29 (20488)
  SS BOND              : bond        0.01022 /  0.62 (    8)
  SS BOND              : angle       1.66387 /  0.95 (   16)
  hydrogen bonds       : bond        0.04477 /  2.90 (  904)
  hydrogen bonds       : angle       4.02590 /  2.87 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 232
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7660 (mtmm) cc_final: 0.6923 (mmtt)
REVERT: A   47 PHE cc_start: 0.6578 (t80) cc_final: 0.6004 (t80)
REVERT: A   50 MET cc_start: 0.6790 (ppp) cc_final: 0.6578 (ppp)
REVERT: A   65 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7573 (tptt)
REVERT: A  370 LYS cc_start: 0.7291 (mmtt) cc_final: 0.7059 (mmtt)
REVERT: A  390 TRP cc_start: 0.8122 (m100) cc_final: 0.7906 (m100)
REVERT: A  436 TRP cc_start: 0.8619 (t60) cc_final: 0.8309 (t60)
REVERT: C  342 PHE cc_start: 0.6332 (m-80) cc_final: 0.5882 (m-10)
REVERT: C  426 MET cc_start: 0.8622 (tpp) cc_final: 0.8383 (tpp)
REVERT: B  168 TYR cc_start: 0.7278 (m-10) cc_final: 0.7048 (m-10)
REVERT: B  426 MET cc_start: 0.8685 (mmt) cc_final: 0.8301 (mmt)
REVERT: B  502 PHE cc_start: 0.5513 (OUTLIER) cc_final: 0.4937 (t80)
REVERT: D   96 ASP cc_start: 0.8028 (t70) cc_final: 0.7503 (t70)
  outliers start: 35
  outliers final: 23
  residues processed: 250
  average time/residue: 0.0945
  time to fit residues: 37.2803
Evaluate side-chains
  224 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  187 GLU
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  386 THR
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  502 PHE
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  427 ILE
Chi-restraints excluded: chain D residue  472 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [103, 115, 80, 68, 45, 136, 90, 0, 174, 170, 133]
   chunk 103 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9980
   chunk 136 optimal weight:    0.6980
   chunk 90 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 174 optimal weight:    0.9990
   chunk 170 optimal weight:    0.4980
   chunk 133 optimal weight:    3.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 192 HIS
B 471 GLN
D 196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.208659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.167516 restraints weight = 19508.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.167398 restraints weight = 17434.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.167741 restraints weight = 15830.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.167636 restraints weight = 15021.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.167701 restraints weight = 14645.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          1.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15152  Z= 0.174
  Angle     :  0.582  14.045  20504  Z= 0.307
  Chirality :  0.040   0.174   2360
  Planarity :  0.004   0.050   2480
  Dihedral  : 11.894 164.663   2208
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.91 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.20), residues: 1760
  helix:  2.39 (0.15), residues: 1088
  sheet: -1.86 (0.39), residues: 176
  loop : -0.08 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 395 
 TYR   0.019   0.002   TYR D 138 
 PHE   0.029   0.002   PHE D 109 
 TRP   0.011   0.001   TRP C 205 
 HIS   0.006   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.17 (15144)
  covalent geometry    : angle       0.57949 /  0.31 (20488)
  SS BOND              : bond        0.01282 /  0.70 (    8)
  SS BOND              : angle       1.84128 /  1.01 (   16)
  hydrogen bonds       : bond        0.04936 /  3.21 (  904)
  hydrogen bonds       : angle       4.12594 /  2.95 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 240
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 PHE cc_start: 0.7226 (t80) cc_final: 0.6786 (t80)
REVERT: A   65 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7853 (mptt)
REVERT: A   96 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7681 (t0)
REVERT: A  374 ASN cc_start: 0.7357 (m-40) cc_final: 0.6581 (p0)
REVERT: C  151 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6312 (m-80)
REVERT: C  316 LEU cc_start: 0.8334 (pp) cc_final: 0.7732 (tp)
REVERT: C  371 LYS cc_start: 0.8585 (ptpt) cc_final: 0.8361 (mtmm)
REVERT: C  418 LEU cc_start: 0.8626 (tp) cc_final: 0.8247 (tt)
REVERT: C  473 GLN cc_start: 0.8218 (mp10) cc_final: 0.7906 (mm-40)
REVERT: B  502 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.5415 (t80)
REVERT: D   96 ASP cc_start: 0.8233 (t70) cc_final: 0.7611 (t70)
  outliers start: 45
  outliers final: 28
  residues processed: 273
  average time/residue: 0.0961
  time to fit residues: 41.4593
Evaluate side-chains
  230 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 CYS
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  151 TYR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  270 ASN
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  502 PHE
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  358 ILE
Chi-restraints excluded: chain D residue  375 TYR
Chi-restraints excluded: chain D residue  427 ILE
Chi-restraints excluded: chain D residue  472 ILE
Chi-restraints excluded: chain D residue  479 VAL
Chi-restraints excluded: chain D residue  511 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [22, 108, 136, 166, 28, 144, 140, 143, 72, 14, 168]
   chunk 22 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0670
   chunk 136 optimal weight:    0.7980
   chunk 166 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 144 optimal weight:    0.7980
   chunk 140 optimal weight:    0.8980
   chunk 143 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 168 optimal weight:    1.9990
   overall best weight:    0.6918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 471 GLN
C  87 ASN
C 192 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.211508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.173318 restraints weight = 19359.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.175583 restraints weight = 21095.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.175452 restraints weight = 14424.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.174844 restraints weight = 12240.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.175137 restraints weight = 13437.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          1.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15152  Z= 0.128
  Angle     :  0.537  11.491  20504  Z= 0.283
  Chirality :  0.039   0.230   2360
  Planarity :  0.003   0.046   2480
  Dihedral  : 11.546 156.914   2208
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 25.86 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.20), residues: 1760
  helix:  2.50 (0.15), residues: 1092
  sheet: -1.98 (0.41), residues: 156
  loop :  0.14 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  59 
 TYR   0.016   0.001   TYR B 216 
 PHE   0.021   0.001   PHE A 293 
 TRP   0.011   0.001   TRP C 205 
 HIS   0.007   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 (15144)
  covalent geometry    : angle       0.53600 /  0.28 (20488)
  SS BOND              : bond        0.00341 /  0.18 (    8)
  SS BOND              : angle       1.18117 /  0.63 (   16)
  hydrogen bonds       : bond        0.04460 /  2.89 (  904)
  hydrogen bonds       : angle       3.97577 /  2.83 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8077 (t80) cc_final: 0.7365 (t80)
REVERT: A  374 ASN cc_start: 0.7345 (m-40) cc_final: 0.6457 (p0)
REVERT: C  418 LEU cc_start: 0.8685 (tp) cc_final: 0.8268 (tt)
REVERT: C  420 PHE cc_start: 0.8629 (t80) cc_final: 0.8371 (t80)
REVERT: C  473 GLN cc_start: 0.8095 (mp10) cc_final: 0.7830 (mm-40)
REVERT: B  502 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.5335 (t80)
REVERT: D   96 ASP cc_start: 0.8178 (t70) cc_final: 0.7491 (t70)
REVERT: D  465 MET cc_start: 0.8637 (tpp) cc_final: 0.8237 (tpp)
  outliers start: 35
  outliers final: 25
  residues processed: 233
  average time/residue: 0.0874
  time to fit residues: 33.2119
Evaluate side-chains
  222 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 196
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  298 ILE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  502 PHE
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  358 ILE
Chi-restraints excluded: chain D residue  375 TYR
Chi-restraints excluded: chain D residue  472 ILE
Chi-restraints excluded: chain D residue  511 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [159, 144, 146, 71, 58, 60, 35, 87, 75, 149, 110]
   chunk 159 optimal weight:    7.9990
   chunk 144 optimal weight:    0.9990
   chunk 146 optimal weight:    3.9990
   chunk 71 optimal weight:    0.3980
   chunk 58 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   chunk 110 optimal weight:   10.0000
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 471 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.211253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.170978 restraints weight = 19307.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.171455 restraints weight = 22912.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.173286 restraints weight = 17250.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.173264 restraints weight = 13602.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.173441 restraints weight = 13663.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          1.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15152  Z= 0.131
  Angle     :  0.536  10.993  20504  Z= 0.283
  Chirality :  0.039   0.302   2360
  Planarity :  0.003   0.044   2480
  Dihedral  : 11.284 153.667   2208
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 26.29 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.20), residues: 1760
  helix:  2.56 (0.15), residues: 1092
  sheet: -1.92 (0.42), residues: 156
  loop :  0.12 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  59 
 TYR   0.017   0.001   TYR A 375 
 PHE   0.024   0.001   PHE C  47 
 TRP   0.011   0.001   TRP C 205 
 HIS   0.004   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 (15144)
  covalent geometry    : angle       0.53534 /  0.28 (20488)
  SS BOND              : bond        0.00417 /  0.23 (    8)
  SS BOND              : angle       1.09709 /  0.58 (   16)
  hydrogen bonds       : bond        0.04383 /  2.86 (  904)
  hydrogen bonds       : angle       3.92708 /  2.79 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 226
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8258 (t80) cc_final: 0.7564 (t80)
REVERT: A   71 LEU cc_start: 0.8278 (tp) cc_final: 0.7975 (tt)
REVERT: A   96 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7475 (t0)
REVERT: C  223 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9154 (mt)
REVERT: C  411 GLN cc_start: 0.7434 (mt0) cc_final: 0.6401 (tp40)
REVERT: C  418 LEU cc_start: 0.8710 (tp) cc_final: 0.8322 (tt)
REVERT: C  465 MET cc_start: 0.8694 (tpp) cc_final: 0.8477 (tpp)
REVERT: B  340 TRP cc_start: 0.7101 (t60) cc_final: 0.6848 (t60)
REVERT: B  473 GLN cc_start: 0.7782 (mp10) cc_final: 0.7558 (mp-120)
REVERT: B  502 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5405 (t80)
REVERT: D   96 ASP cc_start: 0.8222 (t70) cc_final: 0.7501 (t70)
REVERT: D  223 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.9032 (mt)
REVERT: D  465 MET cc_start: 0.8701 (tpp) cc_final: 0.8226 (tpp)
  outliers start: 41
  outliers final: 28
  residues processed: 252
  average time/residue: 0.0923
  time to fit residues: 37.9476
Evaluate side-chains
  233 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  322 PHE
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  502 PHE
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  223 ILE
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  358 ILE
Chi-restraints excluded: chain D residue  375 TYR
Chi-restraints excluded: chain D residue  472 ILE
Chi-restraints excluded: chain D residue  479 VAL
Chi-restraints excluded: chain D residue  511 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [49, 143, 28, 26, 53, 3, 69, 151, 45, 34, 67]
   chunk 49 optimal weight:    0.7980
   chunk 143 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 151 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.8782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.210399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.173140 restraints weight = 19519.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.173871 restraints weight = 22705.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.174808 restraints weight = 18913.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.174223 restraints weight = 16337.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.174391 restraints weight = 15461.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          1.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15152  Z= 0.134
  Angle     :  0.540  10.065  20504  Z= 0.285
  Chirality :  0.039   0.253   2360
  Planarity :  0.003   0.044   2480
  Dihedral  : 11.113 152.229   2208
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 27.09 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.20), residues: 1760
  helix:  2.62 (0.15), residues: 1080
  sheet: -1.90 (0.42), residues: 156
  loop : -0.07 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  82 
 TYR   0.016   0.001   TYR D  48 
 PHE   0.024   0.001   PHE D 210 
 TRP   0.011   0.001   TRP C 205 
 HIS   0.005   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (15144)
  covalent geometry    : angle       0.53946 /  0.28 (20488)
  SS BOND              : bond        0.00426 /  0.21 (    8)
  SS BOND              : angle       1.16384 /  0.62 (   16)
  hydrogen bonds       : bond        0.04372 /  2.84 (  904)
  hydrogen bonds       : angle       3.95774 /  2.80 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 232
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.7871 (t80) cc_final: 0.7200 (t80)
REVERT: A  471 GLN cc_start: 0.8491 (tp40) cc_final: 0.8003 (tp40)
REVERT: C  411 GLN cc_start: 0.7482 (mt0) cc_final: 0.6400 (tp40)
REVERT: C  418 LEU cc_start: 0.8679 (tp) cc_final: 0.8259 (tt)
REVERT: C  465 MET cc_start: 0.8782 (tpp) cc_final: 0.8378 (tpp)
REVERT: C  482 PHE cc_start: 0.8899 (t80) cc_final: 0.8624 (t80)
REVERT: B  216 TYR cc_start: 0.6856 (t80) cc_final: 0.6640 (t80)
REVERT: B  356 MET cc_start: 0.7282 (tpp) cc_final: 0.6845 (mtt)
REVERT: B  473 GLN cc_start: 0.7894 (mp10) cc_final: 0.7681 (mp-120)
REVERT: B  502 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5443 (t80)
REVERT: D   44 ASP cc_start: 0.7480 (m-30) cc_final: 0.7257 (m-30)
REVERT: D   65 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7900 (tptt)
REVERT: D   96 ASP cc_start: 0.8171 (t70) cc_final: 0.7447 (t70)
REVERT: D  465 MET cc_start: 0.8770 (tpp) cc_final: 0.8230 (tpp)
  outliers start: 41
  outliers final: 27
  residues processed: 258
  average time/residue: 0.0895
  time to fit residues: 37.8312
Evaluate side-chains
  249 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 220
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  322 PHE
Chi-restraints excluded: chain C residue  382 LEU
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  502 PHE
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  358 ILE
Chi-restraints excluded: chain D residue  375 TYR
Chi-restraints excluded: chain D residue  472 ILE
Chi-restraints excluded: chain D residue  479 VAL
Chi-restraints excluded: chain D residue  511 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [150, 59, 1, 100, 99, 96, 83, 152, 144, 11, 128]
   chunk 150 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 99 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 152 optimal weight:    1.9990
   chunk 144 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 128 optimal weight:    0.0670
   overall best weight:    1.3522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 HIS
C 166 GLN
C 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.206954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.167453 restraints weight = 19585.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.168189 restraints weight = 22664.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.169829 restraints weight = 19280.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.169633 restraints weight = 15782.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.169728 restraints weight = 14668.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          1.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15152  Z= 0.165
  Angle     :  0.587   9.558  20504  Z= 0.309
  Chirality :  0.040   0.242   2360
  Planarity :  0.003   0.044   2480
  Dihedral  : 11.067 151.415   2208
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 27.70 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.20), residues: 1760
  helix:  2.48 (0.15), residues: 1084
  sheet: -1.86 (0.39), residues: 176
  loop : -0.34 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 319 
 TYR   0.019   0.002   TYR C 375 
 PHE   0.022   0.002   PHE C  47 
 TRP   0.011   0.001   TRP D 390 
 HIS   0.005   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 (15144)
  covalent geometry    : angle       0.58565 /  0.31 (20488)
  SS BOND              : bond        0.00381 /  0.21 (    8)
  SS BOND              : angle       1.33100 /  0.71 (   16)
  hydrogen bonds       : bond        0.04665 /  3.03 (  904)
  hydrogen bonds       : angle       4.05741 /  2.88 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 227
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.7925 (t80) cc_final: 0.7299 (t80)
REVERT: A   96 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7502 (t0)
REVERT: A  471 GLN cc_start: 0.8523 (tp40) cc_final: 0.8057 (tp40)
REVERT: A  502 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5692 (t80)
REVERT: C   75 MET cc_start: 0.6974 (tmm) cc_final: 0.6467 (tmm)
REVERT: C  341 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8056 (tp30)
REVERT: C  362 ILE cc_start: 0.8705 (tt) cc_final: 0.8445 (pt)
REVERT: C  365 MET cc_start: 0.8399 (tpt) cc_final: 0.8146 (mmt)
REVERT: C  411 GLN cc_start: 0.7589 (mt0) cc_final: 0.6643 (tp40)
REVERT: C  418 LEU cc_start: 0.8690 (tp) cc_final: 0.8305 (tt)
REVERT: C  465 MET cc_start: 0.8755 (tpp) cc_final: 0.8380 (tpp)
REVERT: C  482 PHE cc_start: 0.9044 (t80) cc_final: 0.8770 (t80)
REVERT: B  410 MET cc_start: 0.6906 (mmm) cc_final: 0.6589 (tpp)
REVERT: B  471 GLN cc_start: 0.8521 (tp40) cc_final: 0.7901 (tp40)
REVERT: D   44 ASP cc_start: 0.7706 (m-30) cc_final: 0.7242 (m-30)
REVERT: D   65 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7935 (tptt)
REVERT: D   96 ASP cc_start: 0.8227 (t70) cc_final: 0.7534 (t70)
REVERT: D  426 MET cc_start: 0.8720 (tpp) cc_final: 0.8013 (mmt)
  outliers start: 39
  outliers final: 29
  residues processed: 253
  average time/residue: 0.0874
  time to fit residues: 36.1950
Evaluate side-chains
  247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 215
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TYR
Chi-restraints excluded: chain A residue   55 LYS
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  502 PHE
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  322 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  358 ILE
Chi-restraints excluded: chain D residue  375 TYR
Chi-restraints excluded: chain D residue  472 ILE
Chi-restraints excluded: chain D residue  479 VAL
Chi-restraints excluded: chain D residue  511 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [94, 55, 162, 13, 39, 144, 48, 57, 115, 154, 122]
   chunk 94 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 162 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 144 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 154 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 HIS
** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.208040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.169812 restraints weight = 19367.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.170771 restraints weight = 23705.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.172669 restraints weight = 18588.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172403 restraints weight = 13963.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172472 restraints weight = 13896.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          1.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15152  Z= 0.147
  Angle     :  0.571   9.606  20504  Z= 0.301
  Chirality :  0.040   0.269   2360
  Planarity :  0.003   0.045   2480
  Dihedral  : 10.997 150.636   2208
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 28.50 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.20), residues: 1760
  helix:  2.52 (0.15), residues: 1084
  sheet: -2.13 (0.40), residues: 156
  loop : -0.23 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 321 
 TYR   0.017   0.001   TYR D  48 
 PHE   0.023   0.001   PHE A 210 
 TRP   0.010   0.001   TRP C 205 
 HIS   0.005   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 (15144)
  covalent geometry    : angle       0.57038 /  0.30 (20488)
  SS BOND              : bond        0.00406 /  0.23 (    8)
  SS BOND              : angle       1.20542 /  0.64 (   16)
  hydrogen bonds       : bond        0.04468 /  2.90 (  904)
  hydrogen bonds       : angle       4.04682 /  2.86 ( 2688)

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

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

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3520 Ramachandran restraints generated.
    1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 225
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.7879 (t80) cc_final: 0.7204 (t80)
REVERT: A   96 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7455 (t0)
REVERT: A  471 GLN cc_start: 0.8543 (tp40) cc_final: 0.8059 (tp40)
REVERT: C   75 MET cc_start: 0.6862 (tmm) cc_final: 0.6574 (tmm)
REVERT: C  362 ILE cc_start: 0.8694 (tt) cc_final: 0.8439 (pt)
REVERT: C  365 MET cc_start: 0.8379 (tpt) cc_final: 0.8103 (mmt)
REVERT: C  411 GLN cc_start: 0.7555 (mt0) cc_final: 0.6338 (tp40)
REVERT: C  418 LEU cc_start: 0.8674 (tp) cc_final: 0.8323 (tt)
REVERT: C  465 MET cc_start: 0.8771 (tpp) cc_final: 0.8411 (tpp)
REVERT: C  482 PHE cc_start: 0.8921 (t80) cc_final: 0.8720 (t80)
REVERT: B  356 MET cc_start: 0.7353 (tpp) cc_final: 0.6835 (mtt)
REVERT: B  365 MET cc_start: 0.8463 (tpp) cc_final: 0.7933 (mtp)
REVERT: D   44 ASP cc_start: 0.7716 (m-30) cc_final: 0.7294 (m-30)
REVERT: D   96 ASP cc_start: 0.8059 (t70) cc_final: 0.7339 (t70)
REVERT: D  356 MET cc_start: 0.7476 (ttm) cc_final: 0.7148 (mtt)
REVERT: D  426 MET cc_start: 0.8755 (tpp) cc_final: 0.8399 (mmt)
REVERT: D  465 MET cc_start: 0.8753 (tpp) cc_final: 0.8226 (tpp)
  outliers start: 31
  outliers final: 25
  residues processed: 247
  average time/residue: 0.0880
  time to fit residues: 35.8499
Evaluate side-chains
  241 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 215
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  251 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  135 ILE
Chi-restraints excluded: chain D residue  166 GLN
Chi-restraints excluded: chain D residue  274 CYS
Chi-restraints excluded: chain D residue  358 ILE
Chi-restraints excluded: chain D residue  375 TYR
Chi-restraints excluded: chain D residue  472 ILE
Chi-restraints excluded: chain D residue  479 VAL
Chi-restraints excluded: chain D residue  511 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [150, 122, 64, 83, 44, 51, 124, 32, 0, 52, 163]
   chunk 150 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0570
   chunk 64 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 44 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:    0.6980
   chunk 163 optimal weight:    2.9990
   overall best weight:    0.9102

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 HIS
** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.208881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.171149 restraints weight = 19327.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.169705 restraints weight = 22104.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.171613 restraints weight = 22192.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.172263 restraints weight = 18210.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.172292 restraints weight = 16302.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          1.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15152  Z= 0.139
  Angle     :  0.581  10.290  20504  Z= 0.303
  Chirality :  0.041   0.269   2360
  Planarity :  0.004   0.045   2480
  Dihedral  : 10.941 149.951   2208
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 28.99 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.20), residues: 1760
  helix:  2.46 (0.15), residues: 1092
  sheet: -2.14 (0.40), residues: 156
  loop : -0.18 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 321 
 TYR   0.015   0.001   TYR C 375 
 PHE   0.040   0.001   PHE B 210 
 TRP   0.010   0.001   TRP C 205 
 HIS   0.011   0.001   HIS A 257 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 (15144)
  covalent geometry    : angle       0.58032 /  0.30 (20488)
  SS BOND              : bond        0.00367 /  0.20 (    8)
  SS BOND              : angle       1.13646 /  0.60 (   16)
  hydrogen bonds       : bond        0.04444 /  2.88 (  904)
  hydrogen bonds       : angle       4.02726 /  2.85 ( 2688)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2091.65 seconds
wall clock time: 37 minutes 11.05 seconds (2231.05 seconds total)