Starting phenix.real_space_refine
on Fri Aug 22 20:16:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1r_32947/08_2025/7x1r_32947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1r_32947/08_2025/7x1r_32947.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1r_32947/08_2025/7x1r_32947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1r_32947/08_2025/7x1r_32947.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1r_32947/08_2025/7x1r_32947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1r_32947/08_2025/7x1r_32947.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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: 6
    Type Number    sf(0)   Gaussians
     Au      2     10.57       5
     P       4      5.49       5
     S      38      5.16       5
     C    4824      2.51       5
     N    1298      2.21       5
     O    1442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7608
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3750
          Classifications: {'peptide': 485}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {' AU': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1419  SG  CYS A 189      73.629  62.408  61.033  1.00 28.54           S

  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb="AU    AU A 502 " occ=0.30
    residue:
      pdb="AU    AU B 502 " occ=0.30
  Time building chain proxies: 2.52, per 1000 atoms: 0.33
  Number of scatterers: 7608
  At special positions: 0
  Unit cell: (116.8, 104, 76.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Au      2     78.96
     S      38     16.00
     P       4     15.00
     O    1442      8.00
     N    1298      7.00
     C    4824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  64 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  64 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 403.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      36.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 4.346A  pdb=" N   VAL A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 123
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 184'
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 342 through 359
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 430 through 432
      No H-bonds generated for 'chain 'A' and resid 430 through 432'
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'B' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR B  34 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 4.347A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 123
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE B 184 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 184'
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 229 through 243
    Processing helix  chain 'B' and resid 342 through 359
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 430 through 432
      No H-bonds generated for 'chain 'B' and resid 430 through 432'
    Processing helix  chain 'B' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY B 451 " --> pdb=" O   GLU B 447 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 474 through 481
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ARG A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 135 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR A 330 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   PHE A 157 " --> pdb=" O   TYR A 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.828A  pdb=" N   ILE A 178 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN A 272 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ARG A 266 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL A 435 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN A 428 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ARG B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 135 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR B 330 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   PHE B 157 " --> pdb=" O   TYR B 330 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165
    Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179
      removed outlier: 6.829A  pdb=" N   ILE B 178 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN B 272 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ARG B 266 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL B 435 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN B 428 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2486
        1.35 -     1.47: 1858
        1.47 -     1.60: 3368
        1.60 -     1.72: 0
        1.72 -     1.85: 52
  Bond restraints: 7764
  Sorted by residual:
  bond pdb=" O3P FAD B 501 "
       pdb=" P   FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" O5B FAD B 501 "
       pdb=" PA  FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" O5' FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.573  0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 7759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10120
        1.67 -     3.33: 354
        3.33 -     5.00: 33
        5.00 -     6.66: 21
        6.66 -     8.33: 4
  Bond angle restraints: 10532
  Sorted by residual:
  angle pdb=" N   VAL A 305 "
        pdb=" CA  VAL A 305 "
        pdb=" C   VAL A 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" N   VAL B 305 "
        pdb=" CA  VAL B 305 "
        pdb=" C   VAL B 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" C   GLY A 207 "
        pdb=" N   PHE A 208 "
        pdb=" CA  PHE A 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.43    5.71 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   GLY B 207 "
        pdb=" N   PHE B 208 "
        pdb=" CA  PHE B 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.45    5.69 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   ARG B 221 "
        pdb=" N   SER B 222 "
        pdb=" CA  SER B 222 "
      ideal   model   delta    sigma   weight residual
     122.17  117.21    4.96 1.54e+00 4.22e-01 1.04e+01
  ... (remaining 10527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4241
       17.52 -    35.03: 327
       35.03 -    52.55: 66
       52.55 -    70.06: 16
       70.06 -    87.58: 16
  Dihedral angle restraints: 4666
    sinusoidal: 1912
      harmonic: 2754
  Sorted by residual:
  dihedral pdb=" CA  CYS A  59 "
           pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.60  -74.60     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  CYS B  59 "
           pdb=" CB  CYS B  59 "
           pdb=" SG  CYS B  59 "
           pdb=" SG  CYS B  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.55  -74.55     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  ALA B 160 "
           pdb=" C   ALA B 160 "
           pdb=" N   THR B 161 "
           pdb=" CA  THR B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 653
       0.034 -    0.068: 317
       0.068 -    0.102: 141
       0.102 -    0.136: 54
       0.136 -    0.169: 9
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  PHE B 208 "
            pdb=" N   PHE B 208 "
            pdb=" C   PHE B 208 "
            pdb=" CB  PHE B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CA  PHE A 208 "
            pdb=" N   PHE A 208 "
            pdb=" C   PHE A 208 "
            pdb=" CB  PHE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" C2B FAD B 501 "
            pdb=" C1B FAD B 501 "
            pdb=" C3B FAD B 501 "
            pdb=" O2B FAD B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.70    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 170 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B 171 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 171 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 171 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 170 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 171 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 171 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 171 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 208 "    0.011 2.00e-02 2.50e+03   9.59e-03 1.61e+00
        pdb=" CG  PHE B 208 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 208 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 208 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 208 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 969
        2.74 -     3.28: 7362
        3.28 -     3.82: 12429
        3.82 -     4.36: 14855
        4.36 -     4.90: 25607
  Nonbonded interactions: 61222
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 189 "
            pdb="AU    AU B 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" SG  CYS A 189 "
            pdb="AU    AU A 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" O   LEU A  55 "
            pdb=" ND2 ASN A 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   LEU B  55 "
            pdb=" ND2 ASN B 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OG1 THR B 324 "
            pdb=" O   ILE B 329 "
     model   vdw
     2.229 3.040
  ... (remaining 61217 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.320
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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      :  0.007   0.101   7766  Z= 0.334
  Angle     :  0.759   8.330  10536  Z= 0.415
  Chirality :  0.049   0.169   1174
  Planarity :  0.004   0.032   1336
  Dihedral  : 14.250  87.578   2916
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.02 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.24), residues: 966
  helix:  0.38 (0.27), residues: 290
  sheet: -0.35 (0.32), residues: 264
  loop : -1.43 (0.26), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 434 
 TYR   0.015   0.002   TYR B 200 
 PHE   0.022   0.003   PHE B 208 
 TRP   0.006   0.001   TRP B  53 
 HIS   0.005   0.002   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00723 ( 7764)
  covalent geometry    : angle       0.75489 (10532)
  SS BOND              : bond        0.00484 (    2)
  SS BOND              : angle       3.94276 (    4)
  hydrogen bonds       : bond        0.13022 (  336)
  hydrogen bonds       : angle       7.38796 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9074 (mt) cc_final: 0.8771 (mt)
REVERT: A   30 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6698 (mm-30)
REVERT: A   81 GLN cc_start: 0.8038 (tt0) cc_final: 0.7754 (tt0)
REVERT: A   85 ASN cc_start: 0.8588 (m110) cc_final: 0.8295 (m-40)
REVERT: A  139 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7828 (mtp85)
REVERT: A  140 ILE cc_start: 0.8785 (pt) cc_final: 0.8420 (pt)
REVERT: A  222 SER cc_start: 0.8721 (p) cc_final: 0.8229 (t)
REVERT: A  308 LYS cc_start: 0.7830 (mttp) cc_final: 0.7463 (tttm)
REVERT: A  353 LEU cc_start: 0.9041 (tp) cc_final: 0.8723 (tp)
REVERT: A  396 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: A  397 GLU cc_start: 0.7205 (pt0) cc_final: 0.6688 (mt-10)
REVERT: A  450 GLN cc_start: 0.8877 (tp40) cc_final: 0.8558 (tp-100)
REVERT: B   44 VAL cc_start: 0.8996 (p) cc_final: 0.8793 (m)
REVERT: B   85 ASN cc_start: 0.8554 (m110) cc_final: 0.8342 (m-40)
REVERT: B   93 THR cc_start: 0.8339 (t) cc_final: 0.8067 (p)
REVERT: B  192 LYS cc_start: 0.7898 (tttt) cc_final: 0.7447 (ttmm)
REVERT: B  222 SER cc_start: 0.8527 (p) cc_final: 0.8124 (t)
REVERT: B  252 VAL cc_start: 0.9111 (p) cc_final: 0.8899 (m)
REVERT: B  308 LYS cc_start: 0.7904 (mttp) cc_final: 0.7443 (tttm)
REVERT: B  396 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: B  397 GLU cc_start: 0.7094 (pt0) cc_final: 0.6768 (mt-10)
REVERT: B  425 ILE cc_start: 0.8846 (pt) cc_final: 0.8392 (mt)
REVERT: B  450 GLN cc_start: 0.8890 (tp40) cc_final: 0.8554 (tp-100)
  outliers start: 2
  outliers final: 2
  residues processed: 276
  average time/residue: 0.0913
  time to fit residues: 32.6755
Evaluate side-chains
  187 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue  370 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
B 113 ASN
** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.140959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.122175 restraints weight = 8922.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.124369 restraints weight = 6419.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.125902 restraints weight = 5038.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.127146 restraints weight = 4235.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.127672 restraints weight = 3689.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7766  Z= 0.140
  Angle     :  0.573   6.530  10536  Z= 0.305
  Chirality :  0.047   0.150   1174
  Planarity :  0.004   0.051   1336
  Dihedral  :  6.432  46.506   1148
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.91 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.26), residues: 966
  helix:  1.91 (0.29), residues: 294
  sheet:  0.06 (0.33), residues: 256
  loop : -1.13 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 268 
 TYR   0.014   0.002   TYR B  13 
 PHE   0.026   0.002   PHE B 208 
 TRP   0.013   0.001   TRP B  98 
 HIS   0.006   0.002   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7764)
  covalent geometry    : angle       0.56960 (10532)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       3.04083 (    4)
  hydrogen bonds       : bond        0.04166 (  336)
  hydrogen bonds       : angle       5.87843 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 205
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9007 (mt) cc_final: 0.8682 (mt)
REVERT: A   49 LEU cc_start: 0.8570 (mp) cc_final: 0.8366 (mp)
REVERT: A  157 PHE cc_start: 0.8555 (m-80) cc_final: 0.8314 (m-10)
REVERT: A  222 SER cc_start: 0.8706 (p) cc_final: 0.8284 (t)
REVERT: A  308 LYS cc_start: 0.7926 (mttp) cc_final: 0.7458 (tttm)
REVERT: A  450 GLN cc_start: 0.8747 (tp40) cc_final: 0.8392 (tp-100)
REVERT: A  479 PHE cc_start: 0.8685 (m-80) cc_final: 0.8420 (m-80)
REVERT: B   29 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7668 (mttt)
REVERT: B   44 VAL cc_start: 0.9107 (p) cc_final: 0.8890 (m)
REVERT: B  139 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7751 (mtp85)
REVERT: B  157 PHE cc_start: 0.8490 (m-80) cc_final: 0.8238 (m-10)
REVERT: B  192 LYS cc_start: 0.7889 (tttt) cc_final: 0.7537 (ttmm)
REVERT: B  222 SER cc_start: 0.8639 (p) cc_final: 0.8153 (t)
REVERT: B  252 VAL cc_start: 0.8873 (p) cc_final: 0.8661 (m)
REVERT: B  308 LYS cc_start: 0.7877 (mttp) cc_final: 0.7422 (tttm)
REVERT: B  386 SER cc_start: 0.8681 (t) cc_final: 0.8257 (p)
REVERT: B  450 GLN cc_start: 0.8736 (tp40) cc_final: 0.8364 (tp-100)
  outliers start: 15
  outliers final: 9
  residues processed: 216
  average time/residue: 0.0812
  time to fit residues: 24.2562
Evaluate side-chains
  189 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 180
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 129 ASN
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.137057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.119006 restraints weight = 9017.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.119126 restraints weight = 8702.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.120401 restraints weight = 7555.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.120768 restraints weight = 6022.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.121008 restraints weight = 5578.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7766  Z= 0.180
  Angle     :  0.589   6.016  10536  Z= 0.312
  Chirality :  0.047   0.169   1174
  Planarity :  0.004   0.040   1336
  Dihedral  :  6.297  44.886   1148
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 16.29 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.26), residues: 966
  helix:  2.41 (0.31), residues: 282
  sheet:  0.10 (0.32), residues: 256
  loop : -0.96 (0.26), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  84 
 TYR   0.012   0.001   TYR A 358 
 PHE   0.019   0.002   PHE A 208 
 TRP   0.004   0.001   TRP A 114 
 HIS   0.005   0.002   HIS B 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7764)
  covalent geometry    : angle       0.58739 (10532)
  SS BOND              : bond        0.00459 (    2)
  SS BOND              : angle       2.44625 (    4)
  hydrogen bonds       : bond        0.04260 (  336)
  hydrogen bonds       : angle       5.66869 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 185
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  163 GLU cc_start: 0.7666 (pt0) cc_final: 0.7438 (pm20)
REVERT: A  222 SER cc_start: 0.8898 (p) cc_final: 0.8529 (t)
REVERT: A  308 LYS cc_start: 0.8053 (mttp) cc_final: 0.7509 (tttm)
REVERT: A  403 HIS cc_start: 0.8729 (p90) cc_final: 0.8294 (p90)
REVERT: A  479 PHE cc_start: 0.8683 (m-80) cc_final: 0.8200 (m-80)
REVERT: B   29 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7824 (mttt)
REVERT: B   44 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8786 (m)
REVERT: B  139 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7695 (mtp85)
REVERT: B  222 SER cc_start: 0.8886 (p) cc_final: 0.8480 (t)
REVERT: B  252 VAL cc_start: 0.8744 (p) cc_final: 0.8458 (m)
REVERT: B  308 LYS cc_start: 0.8030 (mttp) cc_final: 0.7479 (tttm)
REVERT: B  397 GLU cc_start: 0.7420 (pt0) cc_final: 0.7213 (mt-10)
REVERT: B  403 HIS cc_start: 0.8646 (p90) cc_final: 0.8187 (p90)
  outliers start: 36
  outliers final: 29
  residues processed: 209
  average time/residue: 0.0797
  time to fit residues: 23.0245
Evaluate side-chains
  203 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 173
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  392 GLU
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.133442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.115434 restraints weight = 9384.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.115433 restraints weight = 9885.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.116052 restraints weight = 8783.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.116611 restraints weight = 7092.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.117087 restraints weight = 6382.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7766  Z= 0.244
  Angle     :  0.652   6.110  10536  Z= 0.341
  Chirality :  0.048   0.150   1174
  Planarity :  0.004   0.033   1336
  Dihedral  :  6.490  45.738   1148
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 19.67 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.26), residues: 966
  helix:  2.19 (0.31), residues: 282
  sheet: -0.14 (0.32), residues: 258
  loop : -1.07 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  84 
 TYR   0.016   0.002   TYR A 358 
 PHE   0.021   0.002   PHE B 208 
 TRP   0.005   0.001   TRP B  88 
 HIS   0.007   0.002   HIS A 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 7764)
  covalent geometry    : angle       0.65009 (10532)
  SS BOND              : bond        0.00485 (    2)
  SS BOND              : angle       2.40772 (    4)
  hydrogen bonds       : bond        0.04503 (  336)
  hydrogen bonds       : angle       5.75919 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 177
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   49 LEU cc_start: 0.8655 (mp) cc_final: 0.8381 (mp)
REVERT: A  163 GLU cc_start: 0.7704 (pt0) cc_final: 0.7368 (pt0)
REVERT: A  205 CYS cc_start: 0.7832 (m) cc_final: 0.7433 (m)
REVERT: A  222 SER cc_start: 0.8975 (p) cc_final: 0.8654 (t)
REVERT: A  308 LYS cc_start: 0.8201 (mttp) cc_final: 0.7664 (tttm)
REVERT: B  150 LYS cc_start: 0.8131 (mttt) cc_final: 0.7710 (tptp)
REVERT: B  205 CYS cc_start: 0.8050 (m) cc_final: 0.7818 (m)
REVERT: B  222 SER cc_start: 0.9020 (p) cc_final: 0.8693 (t)
REVERT: B  252 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8408 (m)
REVERT: B  308 LYS cc_start: 0.8205 (mttp) cc_final: 0.7530 (tttm)
REVERT: B  386 SER cc_start: 0.8823 (t) cc_final: 0.8421 (p)
REVERT: B  397 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7069 (mt-10)
  outliers start: 39
  outliers final: 29
  residues processed: 205
  average time/residue: 0.0800
  time to fit residues: 22.9772
Evaluate side-chains
  200 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  392 GLU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0870
   chunk 4 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 79 optimal weight:    0.0070
   chunk 51 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.136383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.119468 restraints weight = 9156.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.119831 restraints weight = 7988.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.120077 restraints weight = 7322.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121938 restraints weight = 6442.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121940 restraints weight = 5107.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7766  Z= 0.139
  Angle     :  0.552   7.072  10536  Z= 0.289
  Chirality :  0.045   0.144   1174
  Planarity :  0.004   0.032   1336
  Dihedral  :  6.175  47.502   1148
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.93 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.27), residues: 966
  helix:  2.46 (0.31), residues: 280
  sheet:  0.06 (0.33), residues: 244
  loop : -0.86 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  84 
 TYR   0.013   0.001   TYR A  13 
 PHE   0.025   0.002   PHE B 208 
 TRP   0.005   0.001   TRP B 407 
 HIS   0.004   0.001   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7764)
  covalent geometry    : angle       0.55096 (10532)
  SS BOND              : bond        0.01043 (    2)
  SS BOND              : angle       1.86321 (    4)
  hydrogen bonds       : bond        0.03775 (  336)
  hydrogen bonds       : angle       5.57541 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 201
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9324 (mp) cc_final: 0.9016 (mm)
REVERT: A  163 GLU cc_start: 0.7557 (pt0) cc_final: 0.7253 (pm20)
REVERT: A  222 SER cc_start: 0.8991 (p) cc_final: 0.8675 (t)
REVERT: A  308 LYS cc_start: 0.8110 (mttp) cc_final: 0.7577 (tmtt)
REVERT: A  362 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (m)
REVERT: A  403 HIS cc_start: 0.8445 (p90) cc_final: 0.8133 (p90)
REVERT: A  479 PHE cc_start: 0.8672 (m-80) cc_final: 0.8185 (m-80)
REVERT: B  139 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7730 (mtp85)
REVERT: B  222 SER cc_start: 0.9056 (p) cc_final: 0.8783 (t)
REVERT: B  289 LEU cc_start: 0.9037 (mt) cc_final: 0.8697 (mp)
REVERT: B  308 LYS cc_start: 0.8128 (mttp) cc_final: 0.7718 (tmtt)
REVERT: B  353 LEU cc_start: 0.8972 (tp) cc_final: 0.8745 (tp)
REVERT: B  433 GLU cc_start: 0.8352 (mp0) cc_final: 0.7758 (pm20)
  outliers start: 34
  outliers final: 24
  residues processed: 225
  average time/residue: 0.0760
  time to fit residues: 24.0569
Evaluate side-chains
  205 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 GLN
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.133780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.116087 restraints weight = 9302.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.115934 restraints weight = 9953.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.116705 restraints weight = 8510.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.117171 restraints weight = 6952.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.117686 restraints weight = 6247.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7766  Z= 0.185
  Angle     :  0.602   7.364  10536  Z= 0.314
  Chirality :  0.047   0.155   1174
  Planarity :  0.004   0.032   1336
  Dihedral  :  6.343  47.178   1148
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 21.05 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.27), residues: 966
  helix:  2.32 (0.31), residues: 282
  sheet: -0.10 (0.33), residues: 244
  loop : -0.93 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  84 
 TYR   0.014   0.002   TYR A  13 
 PHE   0.025   0.002   PHE A 208 
 TRP   0.005   0.001   TRP B  88 
 HIS   0.005   0.002   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7764)
  covalent geometry    : angle       0.59952 (10532)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       3.02012 (    4)
  hydrogen bonds       : bond        0.04029 (  336)
  hydrogen bonds       : angle       5.61951 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 188
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9309 (mp) cc_final: 0.9034 (mm)
REVERT: A  163 GLU cc_start: 0.7596 (pt0) cc_final: 0.7238 (pm20)
REVERT: A  222 SER cc_start: 0.9070 (p) cc_final: 0.8757 (t)
REVERT: A  308 LYS cc_start: 0.8127 (mttp) cc_final: 0.7639 (tmtt)
REVERT: A  334 ASP cc_start: 0.7740 (p0) cc_final: 0.7208 (p0)
REVERT: A  358 TYR cc_start: 0.7577 (m-80) cc_final: 0.7252 (m-80)
REVERT: B   81 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7356 (tt0)
REVERT: B  139 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7695 (mtp85)
REVERT: B  222 SER cc_start: 0.9156 (p) cc_final: 0.8914 (t)
REVERT: B  308 LYS cc_start: 0.8075 (mttp) cc_final: 0.7612 (tmtt)
REVERT: B  433 GLU cc_start: 0.8376 (mp0) cc_final: 0.7976 (pm20)
REVERT: B  447 GLU cc_start: 0.8242 (mp0) cc_final: 0.7887 (mp0)
  outliers start: 45
  outliers final: 39
  residues processed: 218
  average time/residue: 0.0761
  time to fit residues: 23.3046
Evaluate side-chains
  222 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 182
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
A 444 ASN
B 243 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.138591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.120956 restraints weight = 9014.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.120807 restraints weight = 9376.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.121606 restraints weight = 8282.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.122144 restraints weight = 6554.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.122603 restraints weight = 5815.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7766  Z= 0.114
  Angle     :  0.552   9.985  10536  Z= 0.287
  Chirality :  0.045   0.155   1174
  Planarity :  0.004   0.032   1336
  Dihedral  :  6.041  46.265   1148
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.93 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.27), residues: 966
  helix:  2.46 (0.31), residues: 282
  sheet: -0.04 (0.33), residues: 244
  loop : -0.82 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  84 
 TYR   0.012   0.001   TYR A  13 
 PHE   0.029   0.002   PHE A 208 
 TRP   0.008   0.001   TRP A 407 
 HIS   0.008   0.002   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7764)
  covalent geometry    : angle       0.55103 (10532)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       1.73564 (    4)
  hydrogen bonds       : bond        0.03435 (  336)
  hydrogen bonds       : angle       5.46299 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 211
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.9087 (tmmt) cc_final: 0.8879 (ttmt)
REVERT: A   76 LEU cc_start: 0.9219 (mp) cc_final: 0.8900 (mm)
REVERT: A  163 GLU cc_start: 0.7489 (pt0) cc_final: 0.7206 (pm20)
REVERT: A  192 LYS cc_start: 0.8281 (tttt) cc_final: 0.7908 (ttmm)
REVERT: A  205 CYS cc_start: 0.8103 (m) cc_final: 0.7573 (m)
REVERT: A  222 SER cc_start: 0.9076 (p) cc_final: 0.8782 (t)
REVERT: A  243 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6667 (t70)
REVERT: A  308 LYS cc_start: 0.8088 (mttp) cc_final: 0.7531 (tmtt)
REVERT: A  358 TYR cc_start: 0.7535 (m-80) cc_final: 0.7298 (m-80)
REVERT: A  403 HIS cc_start: 0.8412 (p90) cc_final: 0.8107 (p90)
REVERT: A  479 PHE cc_start: 0.8586 (m-80) cc_final: 0.8157 (m-80)
REVERT: B   81 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7545 (tt0)
REVERT: B  139 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7670 (mtp85)
REVERT: B  222 SER cc_start: 0.9110 (p) cc_final: 0.8901 (t)
REVERT: B  280 ILE cc_start: 0.7148 (pt) cc_final: 0.6584 (tt)
REVERT: B  308 LYS cc_start: 0.8079 (mttp) cc_final: 0.7594 (tmtt)
REVERT: B  403 HIS cc_start: 0.8412 (p90) cc_final: 0.8078 (p90)
  outliers start: 39
  outliers final: 28
  residues processed: 236
  average time/residue: 0.0687
  time to fit residues: 23.1132
Evaluate side-chains
  231 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 201
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 82 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0060
   overall best weight:    2.1602

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
B 138 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.135774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.118283 restraints weight = 9198.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.118282 restraints weight = 8787.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.119132 restraints weight = 7814.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.119500 restraints weight = 6479.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.119778 restraints weight = 5927.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7766  Z= 0.167
  Angle     :  0.609  12.111  10536  Z= 0.314
  Chirality :  0.046   0.176   1174
  Planarity :  0.004   0.050   1336
  Dihedral  :  6.232  46.926   1147
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 22.56 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.27), residues: 966
  helix:  2.34 (0.31), residues: 284
  sheet: -0.11 (0.34), residues: 244
  loop : -0.91 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  84 
 TYR   0.012   0.001   TYR A  13 
 PHE   0.023   0.002   PHE B 208 
 TRP   0.007   0.001   TRP B  88 
 HIS   0.004   0.002   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7764)
  covalent geometry    : angle       0.60565 (10532)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       3.21352 (    4)
  hydrogen bonds       : bond        0.03769 (  336)
  hydrogen bonds       : angle       5.45329 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 205
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9314 (mp) cc_final: 0.9024 (mm)
REVERT: A  163 GLU cc_start: 0.7589 (pt0) cc_final: 0.7224 (pm20)
REVERT: A  205 CYS cc_start: 0.8325 (m) cc_final: 0.8002 (m)
REVERT: A  222 SER cc_start: 0.9055 (p) cc_final: 0.8804 (t)
REVERT: A  308 LYS cc_start: 0.8125 (mttp) cc_final: 0.7612 (tmtt)
REVERT: A  479 PHE cc_start: 0.8649 (m-80) cc_final: 0.8396 (m-80)
REVERT: B   81 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7107 (tt0)
REVERT: B  139 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7643 (mtp85)
REVERT: B  222 SER cc_start: 0.9163 (p) cc_final: 0.8947 (t)
REVERT: B  280 ILE cc_start: 0.7230 (pt) cc_final: 0.6669 (tt)
REVERT: B  308 LYS cc_start: 0.8119 (mttp) cc_final: 0.7636 (tmtt)
REVERT: B  425 ILE cc_start: 0.8636 (pt) cc_final: 0.8393 (mt)
REVERT: B  433 GLU cc_start: 0.8501 (mp0) cc_final: 0.8049 (pm20)
  outliers start: 43
  outliers final: 33
  residues processed: 231
  average time/residue: 0.0794
  time to fit residues: 25.5442
Evaluate side-chains
  230 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 88 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 444 ASN
B 138 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.139014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121209 restraints weight = 9146.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.121245 restraints weight = 9377.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.122111 restraints weight = 8187.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.122731 restraints weight = 6530.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.122977 restraints weight = 5803.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7766  Z= 0.118
  Angle     :  0.581  11.410  10536  Z= 0.295
  Chirality :  0.046   0.262   1174
  Planarity :  0.004   0.042   1336
  Dihedral  :  6.043  46.742   1147
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.93 %
    Favored  : 71.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.27), residues: 966
  helix:  2.52 (0.31), residues: 282
  sheet: -0.05 (0.34), residues: 244
  loop : -0.80 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  84 
 TYR   0.009   0.001   TYR B 284 
 PHE   0.027   0.002   PHE A 208 
 TRP   0.005   0.001   TRP B  88 
 HIS   0.005   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7764)
  covalent geometry    : angle       0.57899 (10532)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       2.25495 (    4)
  hydrogen bonds       : bond        0.03322 (  336)
  hydrogen bonds       : angle       5.39115 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9225 (mp) cc_final: 0.8904 (mm)
REVERT: A   86 TYR cc_start: 0.8840 (m-80) cc_final: 0.8526 (m-80)
REVERT: A  150 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7573 (tptp)
REVERT: A  205 CYS cc_start: 0.8110 (m) cc_final: 0.7597 (m)
REVERT: A  222 SER cc_start: 0.9040 (p) cc_final: 0.8825 (t)
REVERT: A  308 LYS cc_start: 0.8114 (mttp) cc_final: 0.7597 (tmtt)
REVERT: A  358 TYR cc_start: 0.7123 (m-80) cc_final: 0.6805 (m-80)
REVERT: A  479 PHE cc_start: 0.8519 (m-80) cc_final: 0.8183 (m-80)
REVERT: B   76 LEU cc_start: 0.9268 (mp) cc_final: 0.8820 (mm)
REVERT: B  139 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7652 (mtp85)
REVERT: B  280 ILE cc_start: 0.7266 (pt) cc_final: 0.6651 (tt)
REVERT: B  308 LYS cc_start: 0.8090 (mttp) cc_final: 0.7623 (tmtt)
REVERT: B  425 ILE cc_start: 0.8616 (pt) cc_final: 0.8388 (mt)
  outliers start: 34
  outliers final: 29
  residues processed: 232
  average time/residue: 0.0780
  time to fit residues: 25.4749
Evaluate side-chains
  223 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 88 optimal weight:    0.4980
   chunk 56 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0060
   chunk 92 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN
B 138 HIS
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.138347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.120905 restraints weight = 9067.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.120673 restraints weight = 9170.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.121067 restraints weight = 8585.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.121583 restraints weight = 7097.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.122232 restraints weight = 6292.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7766  Z= 0.137
  Angle     :  0.607  11.595  10536  Z= 0.311
  Chirality :  0.046   0.263   1174
  Planarity :  0.004   0.045   1336
  Dihedral  :  6.082  46.772   1146
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 24.69 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.27), residues: 966
  helix:  2.43 (0.31), residues: 284
  sheet: -0.11 (0.33), residues: 244
  loop : -0.81 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  84 
 TYR   0.012   0.001   TYR A  13 
 PHE   0.024   0.002   PHE B 208 
 TRP   0.005   0.001   TRP B  88 
 HIS   0.005   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7764)
  covalent geometry    : angle       0.60189 (10532)
  SS BOND              : bond        0.00500 (    2)
  SS BOND              : angle       4.20138 (    4)
  hydrogen bonds       : bond        0.03466 (  336)
  hydrogen bonds       : angle       5.32275 (  948)

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LEU cc_start: 0.9246 (mp) cc_final: 0.8899 (mm)
REVERT: A   86 TYR cc_start: 0.8845 (m-80) cc_final: 0.8542 (m-80)
REVERT: A  205 CYS cc_start: 0.8087 (m) cc_final: 0.7579 (m)
REVERT: A  222 SER cc_start: 0.9110 (p) cc_final: 0.8828 (t)
REVERT: A  308 LYS cc_start: 0.8131 (mttp) cc_final: 0.7602 (tmtt)
REVERT: A  358 TYR cc_start: 0.7262 (m-80) cc_final: 0.6928 (m-80)
REVERT: A  479 PHE cc_start: 0.8548 (m-80) cc_final: 0.8346 (m-80)
REVERT: B   76 LEU cc_start: 0.9307 (mp) cc_final: 0.8922 (mm)
REVERT: B   86 TYR cc_start: 0.8839 (m-80) cc_final: 0.8452 (m-80)
REVERT: B  139 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7657 (mtp85)
REVERT: B  280 ILE cc_start: 0.7258 (pt) cc_final: 0.6657 (tt)
REVERT: B  308 LYS cc_start: 0.8114 (mttp) cc_final: 0.7612 (tmtt)
REVERT: B  362 THR cc_start: 0.7449 (m) cc_final: 0.6969 (t)
REVERT: B  425 ILE cc_start: 0.8624 (pt) cc_final: 0.8403 (mt)
  outliers start: 33
  outliers final: 33
  residues processed: 220
  average time/residue: 0.0809
  time to fit residues: 25.1757
Evaluate side-chains
  228 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 195
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  250 GLN
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  475 CYS
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  475 CYS
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.134377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.116398 restraints weight = 9273.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.116111 restraints weight = 9457.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.117172 restraints weight = 8389.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.117447 restraints weight = 6742.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.117865 restraints weight = 6223.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7766  Z= 0.201
  Angle     :  0.662  12.136  10536  Z= 0.341
  Chirality :  0.048   0.273   1174
  Planarity :  0.004   0.057   1336
  Dihedral  :  6.492  47.483   1146
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 23.81 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.27), residues: 966
  helix:  2.29 (0.31), residues: 282
  sheet: -0.24 (0.34), residues: 244
  loop : -0.85 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  84 
 TYR   0.010   0.001   TYR B 402 
 PHE   0.022   0.002   PHE B 208 
 TRP   0.005   0.001   TRP A 407 
 HIS   0.005   0.002   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 7764)
  covalent geometry    : angle       0.65649 (10532)
  SS BOND              : bond        0.00454 (    2)
  SS BOND              : angle       4.48626 (    4)
  hydrogen bonds       : bond        0.04061 (  336)
  hydrogen bonds       : angle       5.51249 (  948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1275.28 seconds
wall clock time: 22 minutes 48.75 seconds (1368.75 seconds total)