Starting phenix.real_space_refine
on Fri Aug 22 16:56:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyi_42807/08_2025/8uyi_42807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyi_42807/08_2025/8uyi_42807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyi_42807/08_2025/8uyi_42807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyi_42807/08_2025/8uyi_42807.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uyi_42807/08_2025/8uyi_42807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyi_42807/08_2025/8uyi_42807.map"
  }
  resolution = 3.13
  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=   0.018
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
     P       8      5.49       5
     Mg      4      5.21       5
     S      40      5.16       5
     C    3804      2.51       5
     N    1003      2.21       5
     O    1121      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  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: 5980
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2966
          Classifications: {'peptide': 369}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 351}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 2956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2956
          Classifications: {'peptide': 369}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 17, 'TRANS': 351}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'TPO:plan-1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.26, per 1000 atoms: 0.21
  Number of scatterers: 5980
  At special positions: 0
  Unit cell: (116.352, 74.336, 72.72, 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)
     S      40     16.00
     P       8     15.00
     Mg      4     11.99
     O    1121      8.00
     N    1003      7.00
     C    3804      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.40
  Conformation dependent library (CDL) restraints added in 298.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      45.0% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 136
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 203 through 215
      removed outlier: 3.602A  pdb=" N   THR A 215 " --> pdb=" O   MET A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 307 through 328
      removed outlier: 3.769A  pdb=" N   HIS A 328 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 4.042A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 3.578A  pdb=" N   SER A 459 " --> pdb=" O   ARG A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 484
    Processing helix  chain 'A' and resid 486 through 490
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 542 through 554
    Processing helix  chain 'A' and resid 557 through 572
      removed outlier: 3.501A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 138
      removed outlier: 3.541A  pdb=" N   CYS B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 157
      No H-bonds generated for 'chain 'B' and resid 155 through 157'
    Processing helix  chain 'B' and resid 203 through 215
      removed outlier: 3.546A  pdb=" N   THR B 215 " --> pdb=" O   MET B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.564A  pdb=" N   ARG B 302 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.868A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 4.539A  pdb=" N   CYS B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.743A  pdb=" N   TRP B 410 " --> pdb=" O   LYS B 406 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 411 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
      removed outlier: 3.556A  pdb=" N   SER B 459 " --> pdb=" O   ARG B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 485
    Processing helix  chain 'B' and resid 498 through 515
      removed outlier: 3.624A  pdb=" N   LYS B 512 " --> pdb=" O   CYS B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 555
      removed outlier: 3.897A  pdb=" N   ARG B 555 " --> pdb=" O   SER B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 574
    Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 167
      removed outlier: 6.739A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LYS A 167 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ALA A 171 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167
      removed outlier: 5.522A  pdb=" N   LEU B 161 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LYS B 177 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLU B 163 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   LYS B 167 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ALA B 171 " --> pdb=" O   LYS B 167 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER B 251 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   TYR B 250 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.521A  pdb=" N   CYS B 295 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372

    266 hydrogen bonds defined for protein.
    765 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: 0.85

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1895
        1.34 -     1.46: 1213
        1.46 -     1.58: 2905
        1.58 -     1.69: 20
        1.69 -     1.81: 62
  Bond restraints: 6095
  Sorted by residual:
  bond pdb=" OG1 TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.611  0.106 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" OG1 TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.611  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" O2P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" O3P TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" O3P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  ... (remaining 6090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 8170
        2.40 -     4.79: 69
        4.79 -     7.19: 20
        7.19 -     9.59: 2
        9.59 -    11.99: 4
  Bond angle restraints: 8265
  Sorted by residual:
  angle pdb=" CB  TPO A 305 "
        pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.32   11.99 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" C   THR B 215 "
        pdb=" N   VAL B 216 "
        pdb=" CA  VAL B 216 "
      ideal   model   delta    sigma   weight residual
     120.33  123.43   -3.10 8.00e-01 1.56e+00 1.50e+01
  angle pdb=" CB  TPO B 305 "
        pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
      ideal   model   delta    sigma   weight residual
     119.31  108.58   10.73 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
        pdb=" O1P TPO B 305 "
      ideal   model   delta    sigma   weight residual
     100.43  111.06  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
        pdb=" O1P TPO A 305 "
      ideal   model   delta    sigma   weight residual
     100.43  110.11   -9.68 3.00e+00 1.11e-01 1.04e+01
  ... (remaining 8260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.23: 3638
       33.23 -    66.46: 60
       66.46 -    99.69: 2
       99.69 -   132.91: 0
      132.91 -   166.14: 2
  Dihedral angle restraints: 3702
    sinusoidal: 1516
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" C5' ADP A 601 "
           pdb=" O5' ADP A 601 "
           pdb=" PA  ADP A 601 "
           pdb=" O2A ADP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  133.86  166.14     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" O1B ADP A 601 "
           pdb=" O3A ADP A 601 "
           pdb=" PB  ADP A 601 "
           pdb=" PA  ADP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   89.85 -149.86     1      2.00e+01 2.50e-03 4.48e+01
  dihedral pdb=" O2A ADP B 601 "
           pdb=" O3A ADP B 601 "
           pdb=" PA  ADP B 601 "
           pdb=" PB  ADP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   24.11  -84.11     1      2.00e+01 2.50e-03 2.15e+01
  ... (remaining 3699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 597
       0.031 -    0.062: 220
       0.062 -    0.093: 69
       0.093 -    0.124: 38
       0.124 -    0.155: 8
  Chirality restraints: 932
  Sorted by residual:
  chirality pdb=" CA  ILE A 450 "
            pdb=" N   ILE A 450 "
            pdb=" C   ILE A 450 "
            pdb=" CB  ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  ILE A 246 "
            pdb=" N   ILE A 246 "
            pdb=" C   ILE A 246 "
            pdb=" CB  ILE A 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  ILE B 246 "
            pdb=" N   ILE B 246 "
            pdb=" C   ILE B 246 "
            pdb=" CB  ILE B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 929 not shown)

  Planarity restraints: 1029
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 243 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO A 244 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 244 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 244 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 243 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO B 244 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO B 451 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1026 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 67
        2.63 -     3.19: 4804
        3.19 -     3.76: 8944
        3.76 -     4.33: 12969
        4.33 -     4.90: 21241
  Nonbonded interactions: 48025
  Sorted by model distance:
  nonbonded pdb=" O2A ADP B 601 "
            pdb="MG    MG B 603 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OD1 ASP B 357 "
            pdb="MG    MG B 602 "
     model   vdw
     2.073 2.170
  nonbonded pdb=" OD1 ASN A 339 "
            pdb="MG    MG A 603 "
     model   vdw
     2.105 2.170
  nonbonded pdb=" OD1 ASN B 339 "
            pdb="MG    MG B 603 "
     model   vdw
     2.205 2.170
  nonbonded pdb=" OD2 ASP A 357 "
            pdb="MG    MG A 603 "
     model   vdw
     2.240 2.170
  ... (remaining 48020 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 122 through 223 or resid 237 through 603))
  selection = (chain 'B' and (resid 122 through 136 or resid 148 through 572 or resid 601 thro \ 
ugh 603))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.400
  Find NCS groups from input model:        0.100
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
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      :  0.004   0.106   6095  Z= 0.200
  Angle     :  0.673  11.987   8265  Z= 0.341
  Chirality :  0.041   0.155    932
  Planarity :  0.005   0.043   1029
  Dihedral  : 12.678 166.142   2272
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  4.92 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.29), residues: 698
  helix: -0.70 (0.24), residues: 299
  sheet: -0.09 (0.56), residues: 92
  loop : -0.35 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 469 
 TYR   0.007   0.001   TYR B 438 
 PHE   0.011   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 489 
 HIS   0.003   0.001   HIS A 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6095)
  covalent geometry    : angle       0.67334 ( 8265)
  hydrogen bonds       : bond        0.25991 (  266)
  hydrogen bonds       : angle       7.54208 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7676 (mt) cc_final: 0.7309 (mm)
REVERT: A  194 MET cc_start: 0.8047 (ttt) cc_final: 0.7398 (tmm)
REVERT: A  197 ASN cc_start: 0.8029 (t0) cc_final: 0.7664 (t0)
REVERT: A  219 MET cc_start: 0.8061 (mtt) cc_final: 0.7833 (mtt)
REVERT: A  236 PHE cc_start: 0.5701 (m-80) cc_final: 0.5054 (m-80)
REVERT: A  318 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: A  334 ASP cc_start: 0.7492 (t70) cc_final: 0.7116 (t0)
REVERT: A  433 LEU cc_start: 0.8041 (mt) cc_final: 0.7794 (mp)
REVERT: A  436 LYS cc_start: 0.7240 (tttt) cc_final: 0.6742 (ttpt)
REVERT: A  452 PHE cc_start: 0.7155 (t80) cc_final: 0.6787 (t80)
REVERT: A  456 ASN cc_start: 0.8273 (m-40) cc_final: 0.7861 (m-40)
REVERT: A  558 LEU cc_start: 0.7429 (tp) cc_final: 0.7100 (tp)
REVERT: B  129 TRP cc_start: 0.7335 (t60) cc_final: 0.6833 (t60)
REVERT: B  298 LYS cc_start: 0.7700 (tttt) cc_final: 0.7418 (ttpt)
REVERT: B  377 ASP cc_start: 0.5506 (t70) cc_final: 0.5239 (t0)
REVERT: B  393 ASN cc_start: 0.7864 (m-40) cc_final: 0.7141 (m110)
REVERT: B  401 TRP cc_start: 0.7061 (m100) cc_final: 0.6809 (m-90)
REVERT: B  403 ASN cc_start: 0.8165 (t0) cc_final: 0.7454 (p0)
REVERT: B  418 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7227 (tt0)
REVERT: B  436 LYS cc_start: 0.6073 (tttt) cc_final: 0.4809 (mptt)
REVERT: B  439 LYS cc_start: 0.7546 (mttt) cc_final: 0.7313 (mtpt)
REVERT: B  442 ASP cc_start: 0.8205 (m-30) cc_final: 0.7741 (m-30)
REVERT: B  471 ASP cc_start: 0.7209 (m-30) cc_final: 0.6912 (m-30)
REVERT: B  501 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7540 (mt-10)
REVERT: B  541 ARG cc_start: 0.5720 (mtt-85) cc_final: 0.5463 (mtm-85)
REVERT: B  566 LYS cc_start: 0.8027 (tttt) cc_final: 0.7765 (ttpp)
  outliers start: 7
  outliers final: 2
  residues processed: 199
  average time/residue: 0.0870
  time to fit residues: 21.9764
Evaluate side-chains
  145 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 142
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain B residue  500 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0170
   chunk 27 optimal weight:    0.0570
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 GLN
B 328 HIS
B 378 GLN
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.194013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.170412 restraints weight = 6968.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.03
r_work: 0.3828 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6095  Z= 0.109
  Angle     :  0.564   6.145   8265  Z= 0.271
  Chirality :  0.039   0.130    932
  Planarity :  0.004   0.033   1029
  Dihedral  :  9.578 140.065    827
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.38 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.31), residues: 698
  helix:  1.20 (0.28), residues: 302
  sheet: -0.23 (0.49), residues: 101
  loop :  0.03 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 302 
 TYR   0.015   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 452 
 TRP   0.006   0.001   TRP A 567 
 HIS   0.012   0.002   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6095)
  covalent geometry    : angle       0.56382 ( 8265)
  hydrogen bonds       : bond        0.04465 (  266)
  hydrogen bonds       : angle       4.54925 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7955 (mt) cc_final: 0.7657 (mm)
REVERT: A  199 ASP cc_start: 0.8410 (m-30) cc_final: 0.8075 (m-30)
REVERT: A  204 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (m)
REVERT: A  236 PHE cc_start: 0.7199 (m-80) cc_final: 0.6862 (m-80)
REVERT: A  249 MET cc_start: 0.8015 (ttm) cc_final: 0.7634 (ttm)
REVERT: A  318 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8434 (tt)
REVERT: A  384 ARG cc_start: 0.8348 (mtm110) cc_final: 0.8094 (mtm110)
REVERT: A  418 GLU cc_start: 0.6365 (mt-10) cc_final: 0.5928 (mt-10)
REVERT: A  572 HIS cc_start: 0.6562 (m-70) cc_final: 0.6256 (m170)
REVERT: B  129 TRP cc_start: 0.7503 (t60) cc_final: 0.7172 (t60)
REVERT: B  213 ARG cc_start: 0.8244 (mtt180) cc_final: 0.8036 (mtt-85)
REVERT: B  393 ASN cc_start: 0.8437 (m-40) cc_final: 0.8195 (m110)
REVERT: B  423 ASP cc_start: 0.7961 (m-30) cc_final: 0.7693 (t70)
REVERT: B  436 LYS cc_start: 0.7451 (tttt) cc_final: 0.6195 (mppt)
  outliers start: 14
  outliers final: 6
  residues processed: 156
  average time/residue: 0.0771
  time to fit residues: 15.6720
Evaluate side-chains
  136 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 29 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN
B 572 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.191942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.168802 restraints weight = 6871.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 1.87
r_work: 0.3806 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3664 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6095  Z= 0.112
  Angle     :  0.547   6.210   8265  Z= 0.261
  Chirality :  0.039   0.130    932
  Planarity :  0.004   0.032   1029
  Dihedral  :  8.831 125.949    824
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.31 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.32), residues: 698
  helix:  1.87 (0.30), residues: 303
  sheet: -0.17 (0.48), residues: 101
  loop :  0.12 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 292 
 TYR   0.014   0.001   TYR A 482 
 PHE   0.012   0.001   PHE A 287 
 TRP   0.005   0.001   TRP A 505 
 HIS   0.011   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6095)
  covalent geometry    : angle       0.54721 ( 8265)
  hydrogen bonds       : bond        0.03867 (  266)
  hydrogen bonds       : angle       4.27318 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7966 (mt) cc_final: 0.7670 (mm)
REVERT: A  199 ASP cc_start: 0.8404 (m-30) cc_final: 0.8104 (m-30)
REVERT: A  236 PHE cc_start: 0.7382 (m-80) cc_final: 0.7113 (m-80)
REVERT: A  318 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8520 (tt)
REVERT: A  384 ARG cc_start: 0.8346 (mtm110) cc_final: 0.8089 (mtm110)
REVERT: A  418 GLU cc_start: 0.6500 (mt-10) cc_final: 0.6186 (mt-10)
REVERT: A  570 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7727 (tt0)
REVERT: B  129 TRP cc_start: 0.7528 (t60) cc_final: 0.7186 (t60)
REVERT: B  436 LYS cc_start: 0.7433 (tttt) cc_final: 0.6161 (mptt)
  outliers start: 13
  outliers final: 5
  residues processed: 136
  average time/residue: 0.0777
  time to fit residues: 13.6496
Evaluate side-chains
  127 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0010
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.0150

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.190864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.166804 restraints weight = 6930.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.95
r_work: 0.3785 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6095  Z= 0.124
  Angle     :  0.574  14.010   8265  Z= 0.269
  Chirality :  0.040   0.131    932
  Planarity :  0.004   0.033   1029
  Dihedral  :  8.095 117.188    824
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.46 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.33), residues: 698
  helix:  2.07 (0.30), residues: 303
  sheet: -0.40 (0.47), residues: 109
  loop :  0.13 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 213 
 TYR   0.017   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 253 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.010   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6095)
  covalent geometry    : angle       0.57449 ( 8265)
  hydrogen bonds       : bond        0.03557 (  266)
  hydrogen bonds       : angle       4.16921 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7991 (mt) cc_final: 0.7691 (mm)
REVERT: A  199 ASP cc_start: 0.8399 (m-30) cc_final: 0.8177 (m-30)
REVERT: A  236 PHE cc_start: 0.7367 (m-80) cc_final: 0.7126 (m-80)
REVERT: A  318 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8530 (tt)
REVERT: A  418 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6288 (mt-10)
REVERT: A  452 PHE cc_start: 0.7598 (t80) cc_final: 0.7376 (t80)
REVERT: A  557 ARG cc_start: 0.7838 (mmt90) cc_final: 0.7608 (mtm180)
REVERT: A  570 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7779 (tt0)
REVERT: B  129 TRP cc_start: 0.7580 (t60) cc_final: 0.7221 (t60)
REVERT: B  436 LYS cc_start: 0.7615 (tttt) cc_final: 0.6318 (mppt)
REVERT: B  558 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8206 (mp)
  outliers start: 17
  outliers final: 13
  residues processed: 133
  average time/residue: 0.0805
  time to fit residues: 13.8636
Evaluate side-chains
  134 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 3 optimal weight:   20.0000
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0870
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.5564

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 326 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.188122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.164442 restraints weight = 7061.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 1.94
r_work: 0.3760 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6095  Z= 0.161
  Angle     :  0.606  14.921   8265  Z= 0.286
  Chirality :  0.042   0.158    932
  Planarity :  0.004   0.035   1029
  Dihedral  :  7.933 117.680    824
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.46 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.33), residues: 698
  helix:  2.03 (0.31), residues: 303
  sheet: -0.51 (0.46), residues: 109
  loop :  0.09 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 213 
 TYR   0.017   0.001   TYR A 482 
 PHE   0.009   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.009   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6095)
  covalent geometry    : angle       0.60630 ( 8265)
  hydrogen bonds       : bond        0.03785 (  266)
  hydrogen bonds       : angle       4.27771 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8062 (mt) cc_final: 0.7757 (mm)
REVERT: A  199 ASP cc_start: 0.8416 (m-30) cc_final: 0.8193 (m-30)
REVERT: A  221 TYR cc_start: 0.8163 (m-80) cc_final: 0.7901 (m-80)
REVERT: A  236 PHE cc_start: 0.7380 (m-80) cc_final: 0.7123 (m-80)
REVERT: A  318 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8570 (tt)
REVERT: A  557 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7669 (mtm180)
REVERT: B  129 TRP cc_start: 0.7608 (t60) cc_final: 0.7279 (t60)
REVERT: B  436 LYS cc_start: 0.7694 (tttt) cc_final: 0.6296 (mppt)
REVERT: B  558 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8252 (mp)
  outliers start: 21
  outliers final: 14
  residues processed: 139
  average time/residue: 0.0815
  time to fit residues: 14.4361
Evaluate side-chains
  131 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 421 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.191007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.167265 restraints weight = 6907.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.91
r_work: 0.3785 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6095  Z= 0.110
  Angle     :  0.568  15.573   8265  Z= 0.266
  Chirality :  0.040   0.210    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.704 115.262    824
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.08 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.33), residues: 698
  helix:  2.16 (0.30), residues: 303
  sheet: -0.02 (0.49), residues: 99
  loop : -0.02 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 213 
 TYR   0.016   0.001   TYR A 482 
 PHE   0.009   0.001   PHE A 253 
 TRP   0.006   0.001   TRP B 567 
 HIS   0.010   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6095)
  covalent geometry    : angle       0.56821 ( 8265)
  hydrogen bonds       : bond        0.03249 (  266)
  hydrogen bonds       : angle       4.10186 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8026 (mt) cc_final: 0.7733 (mm)
REVERT: A  199 ASP cc_start: 0.8370 (m-30) cc_final: 0.8156 (m-30)
REVERT: A  221 TYR cc_start: 0.8127 (m-80) cc_final: 0.7844 (m-80)
REVERT: A  236 PHE cc_start: 0.7401 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  318 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8560 (tt)
REVERT: B  129 TRP cc_start: 0.7574 (t60) cc_final: 0.7257 (t60)
REVERT: B  436 LYS cc_start: 0.7656 (tttt) cc_final: 0.6225 (mppt)
  outliers start: 19
  outliers final: 14
  residues processed: 134
  average time/residue: 0.0835
  time to fit residues: 14.6247
Evaluate side-chains
  130 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0050
   chunk 17 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 64 optimal weight:    0.4980
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.189894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.165714 restraints weight = 6892.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 1.96
r_work: 0.3771 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6095  Z= 0.128
  Angle     :  0.591  15.945   8265  Z= 0.276
  Chirality :  0.041   0.174    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.582 115.136    824
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.38 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.33), residues: 698
  helix:  2.14 (0.30), residues: 303
  sheet: -0.08 (0.48), residues: 99
  loop : -0.03 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 213 
 TYR   0.016   0.001   TYR A 482 
 PHE   0.009   0.001   PHE A 253 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.010   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6095)
  covalent geometry    : angle       0.59079 ( 8265)
  hydrogen bonds       : bond        0.03357 (  266)
  hydrogen bonds       : angle       4.13608 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8009 (mt) cc_final: 0.7734 (mm)
REVERT: A  199 ASP cc_start: 0.8414 (m-30) cc_final: 0.8178 (m-30)
REVERT: A  221 TYR cc_start: 0.8159 (m-80) cc_final: 0.7870 (m-80)
REVERT: A  236 PHE cc_start: 0.7370 (m-80) cc_final: 0.7144 (m-80)
REVERT: A  318 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8571 (tt)
REVERT: A  334 ASP cc_start: 0.7617 (t0) cc_final: 0.7239 (t0)
REVERT: B  129 TRP cc_start: 0.7572 (t60) cc_final: 0.7247 (t60)
REVERT: B  290 MET cc_start: 0.8737 (mtm) cc_final: 0.8515 (mtm)
REVERT: B  423 ASP cc_start: 0.8032 (t0) cc_final: 0.7046 (m-30)
REVERT: B  436 LYS cc_start: 0.7653 (tttt) cc_final: 0.6217 (mppt)
  outliers start: 20
  outliers final: 17
  residues processed: 134
  average time/residue: 0.0764
  time to fit residues: 13.4842
Evaluate side-chains
  136 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.191541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.167631 restraints weight = 6951.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.93
r_work: 0.3792 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6095  Z= 0.108
  Angle     :  0.575  16.073   8265  Z= 0.269
  Chirality :  0.040   0.156    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.463 112.787    824
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.00 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.33), residues: 698
  helix:  2.25 (0.30), residues: 303
  sheet: -0.01 (0.49), residues: 99
  loop : -0.01 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 213 
 TYR   0.015   0.001   TYR A 482 
 PHE   0.009   0.001   PHE A 253 
 TRP   0.007   0.001   TRP B 567 
 HIS   0.010   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6095)
  covalent geometry    : angle       0.57511 ( 8265)
  hydrogen bonds       : bond        0.03109 (  266)
  hydrogen bonds       : angle       4.04785 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7986 (mt) cc_final: 0.7717 (mm)
REVERT: A  199 ASP cc_start: 0.8301 (m-30) cc_final: 0.8077 (m-30)
REVERT: A  221 TYR cc_start: 0.8112 (m-80) cc_final: 0.7790 (m-80)
REVERT: A  236 PHE cc_start: 0.7407 (m-80) cc_final: 0.7195 (m-80)
REVERT: A  318 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8565 (tt)
REVERT: A  334 ASP cc_start: 0.7569 (t0) cc_final: 0.7218 (t0)
REVERT: A  450 ILE cc_start: 0.8008 (mt) cc_final: 0.7737 (tt)
REVERT: B  129 TRP cc_start: 0.7552 (t60) cc_final: 0.7256 (t60)
REVERT: B  423 ASP cc_start: 0.8003 (t0) cc_final: 0.7050 (m-30)
REVERT: B  436 LYS cc_start: 0.7682 (tttt) cc_final: 0.6271 (mppt)
  outliers start: 17
  outliers final: 14
  residues processed: 131
  average time/residue: 0.0846
  time to fit residues: 14.4537
Evaluate side-chains
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 456 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.187846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.163368 restraints weight = 7028.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 1.97
r_work: 0.3747 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6095  Z= 0.168
  Angle     :  0.635  16.669   8265  Z= 0.299
  Chirality :  0.043   0.149    932
  Planarity :  0.004   0.035   1029
  Dihedral  :  7.621 111.877    824
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.85 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.33), residues: 698
  helix:  2.04 (0.30), residues: 303
  sheet: -0.09 (0.49), residues: 99
  loop : -0.13 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 213 
 TYR   0.018   0.001   TYR A 482 
 PHE   0.008   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.010   0.002   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6095)
  covalent geometry    : angle       0.63504 ( 8265)
  hydrogen bonds       : bond        0.03728 (  266)
  hydrogen bonds       : angle       4.25155 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8028 (mt) cc_final: 0.7737 (mm)
REVERT: A  199 ASP cc_start: 0.8381 (m-30) cc_final: 0.8164 (m-30)
REVERT: A  221 TYR cc_start: 0.8246 (m-80) cc_final: 0.7970 (m-80)
REVERT: A  318 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8603 (tt)
REVERT: A  334 ASP cc_start: 0.7762 (t0) cc_final: 0.7354 (t0)
REVERT: A  450 ILE cc_start: 0.7972 (mt) cc_final: 0.7680 (tt)
REVERT: B  129 TRP cc_start: 0.7600 (t60) cc_final: 0.7282 (t60)
  outliers start: 21
  outliers final: 17
  residues processed: 132
  average time/residue: 0.0802
  time to fit residues: 13.8843
Evaluate side-chains
  133 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  456 ASN
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0010
   chunk 19 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0020
   chunk 57 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.191187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.167007 restraints weight = 6884.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 1.95
r_work: 0.3787 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6095  Z= 0.104
  Angle     :  0.592  16.965   8265  Z= 0.277
  Chirality :  0.040   0.145    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.464 110.065    824
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.77 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.33), residues: 698
  helix:  2.21 (0.31), residues: 303
  sheet: -0.00 (0.49), residues: 99
  loop : -0.05 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 213 
 TYR   0.015   0.001   TYR A 482 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.009   0.001   TRP B 567 
 HIS   0.010   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6095)
  covalent geometry    : angle       0.59156 ( 8265)
  hydrogen bonds       : bond        0.03234 (  266)
  hydrogen bonds       : angle       4.08000 (  765)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.8000 (mt) cc_final: 0.7706 (mm)
REVERT: A  199 ASP cc_start: 0.8318 (m-30) cc_final: 0.8102 (m-30)
REVERT: A  221 TYR cc_start: 0.8179 (m-80) cc_final: 0.7904 (m-80)
REVERT: A  318 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8560 (tt)
REVERT: A  334 ASP cc_start: 0.7601 (t0) cc_final: 0.7255 (t0)
REVERT: B  129 TRP cc_start: 0.7579 (t60) cc_final: 0.7276 (t60)
REVERT: B  423 ASP cc_start: 0.7966 (t0) cc_final: 0.7072 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0845
  time to fit residues: 13.5263
Evaluate side-chains
  126 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.187476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163069 restraints weight = 6944.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.94
r_work: 0.3742 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6095  Z= 0.176
  Angle     :  0.641  17.068   8265  Z= 0.304
  Chirality :  0.043   0.150    932
  Planarity :  0.004   0.035   1029
  Dihedral  :  7.563 108.292    824
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.46 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.33), residues: 698
  helix:  2.09 (0.30), residues: 302
  sheet: -0.11 (0.49), residues: 99
  loop : -0.12 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 213 
 TYR   0.017   0.001   TYR A 482 
 PHE   0.009   0.002   PHE B 399 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.011   0.002   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6095)
  covalent geometry    : angle       0.64113 ( 8265)
  hydrogen bonds       : bond        0.03769 (  266)
  hydrogen bonds       : angle       4.26943 (  765)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1581.54 seconds
wall clock time: 27 minutes 43.10 seconds (1663.10 seconds total)