Starting phenix.real_space_refine
on Tue Feb 11 08:49:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tjx_10514/02_2025/6tjx_10514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tjx_10514/02_2025/6tjx_10514.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tjx_10514/02_2025/6tjx_10514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tjx_10514/02_2025/6tjx_10514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tjx_10514/02_2025/6tjx_10514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tjx_10514/02_2025/6tjx_10514.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    3042      2.51       5
     N     906      2.21       5
     O     918      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4878
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.65, per 1000 atoms: 0.54
  Number of scatterers: 4878
  At special positions: 0
  Unit cell: (180.55, 141.45, 32.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     918      8.00
     N     906      7.00
     C    3042      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: 1.02
  Conformation dependent library (CDL) restraints added in 563.1 milliseconds
  

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1128

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 30.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 279
      removed outlier: 6.280A  pdb=" N   GLN A 276 " --> pdb=" O   ILE E 277 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   ASN E 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   ILE A 278 " --> pdb=" O   ASN E 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 286 through 289
      removed outlier: 6.204A  pdb=" N   VAL A 287 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.427A  pdb=" N   VAL A 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   VAL C 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 318 through 319
      removed outlier: 6.663A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 327 through 330
      removed outlier: 6.823A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 339
      removed outlier: 6.259A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.519A  pdb=" N   ASP A 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.208A  pdb=" N   VAL A 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   LYS C 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   SER A 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.659A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 377
      removed outlier: 6.597A  pdb=" N   LYS A 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   THR C 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   GLU A 372 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LYS C 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   HIS A 374 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   THR C 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU A 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 275 through 279
      removed outlier: 6.240A  pdb=" N   GLN B 276 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ASN F 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   ILE B 278 " --> pdb=" O   ASN F 279 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 286 through 289
      removed outlier: 6.191A  pdb=" N   VAL B 287 " --> pdb=" O   GLN D 288 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.382A  pdb=" N   VAL B 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   VAL D 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 318 through 319
      removed outlier: 6.645A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 327 through 330
      removed outlier: 6.825A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 336 through 339
      removed outlier: 6.294A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.514A  pdb=" N   ASP B 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.231A  pdb=" N   VAL B 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   LYS D 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER B 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 360 through 362
    Processing sheet with id=AC2, first strand: chain 'D' and resid 369 through 377
      removed outlier: 6.684A  pdb=" N   LYS B 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   THR D 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   GLU B 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   LYS D 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   HIS B 374 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   THR D 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 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: 1.28

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.21 -     1.32: 1006
        1.32 -     1.44: 926
        1.44 -     1.55: 3000
        1.55 -     1.67: 0
        1.67 -     1.78: 12
  Bond restraints: 4944
  Sorted by residual:
  bond pdb=" CD  LYS E 311 "
       pdb=" CE  LYS E 311 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 4.00e+00
  bond pdb=" CD  LYS A 311 "
       pdb=" CE  LYS A 311 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 3.96e+00
  bond pdb=" CD  LYS C 311 "
       pdb=" CE  LYS C 311 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 3.94e+00
  bond pdb=" CD  LYS F 311 "
       pdb=" CE  LYS F 311 "
    ideal  model  delta    sigma   weight residual
    1.520  1.461  0.059 3.00e-02 1.11e+03 3.93e+00
  bond pdb=" CD  LYS D 311 "
       pdb=" CE  LYS D 311 "
    ideal  model  delta    sigma   weight residual
    1.520  1.461  0.059 3.00e-02 1.11e+03 3.89e+00
  ... (remaining 4939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 6119
        1.90 -     3.79: 408
        3.79 -     5.68: 45
        5.68 -     7.58: 28
        7.58 -     9.47: 6
  Bond angle restraints: 6606
  Sorted by residual:
  angle pdb=" N   ASP B 348 "
        pdb=" CA  ASP B 348 "
        pdb=" C   ASP B 348 "
      ideal   model   delta    sigma   weight residual
     108.45  112.68   -4.23 1.26e+00 6.30e-01 1.13e+01
  angle pdb=" N   ASP C 348 "
        pdb=" CA  ASP C 348 "
        pdb=" C   ASP C 348 "
      ideal   model   delta    sigma   weight residual
     108.45  112.68   -4.23 1.26e+00 6.30e-01 1.13e+01
  angle pdb=" N   ASP D 348 "
        pdb=" CA  ASP D 348 "
        pdb=" C   ASP D 348 "
      ideal   model   delta    sigma   weight residual
     108.45  112.67   -4.22 1.26e+00 6.30e-01 1.12e+01
  angle pdb=" N   ASP A 348 "
        pdb=" CA  ASP A 348 "
        pdb=" C   ASP A 348 "
      ideal   model   delta    sigma   weight residual
     108.45  112.67   -4.22 1.26e+00 6.30e-01 1.12e+01
  angle pdb=" N   ASP F 348 "
        pdb=" CA  ASP F 348 "
        pdb=" C   ASP F 348 "
      ideal   model   delta    sigma   weight residual
     108.45  112.65   -4.20 1.26e+00 6.30e-01 1.11e+01
  ... (remaining 6601 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.32: 2437
        8.32 -    16.65: 436
       16.65 -    24.97: 121
       24.97 -    33.29: 42
       33.29 -    41.61: 18
  Dihedral angle restraints: 3054
    sinusoidal: 1284
      harmonic: 1770
  Sorted by residual:
  dihedral pdb=" CA  GLY D 323 "
           pdb=" C   GLY D 323 "
           pdb=" N   SER D 324 "
           pdb=" CA  SER D 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.27   29.73     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  GLY B 323 "
           pdb=" C   GLY B 323 "
           pdb=" N   SER B 324 "
           pdb=" CA  SER B 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.31   29.69     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  GLY A 323 "
           pdb=" C   GLY A 323 "
           pdb=" N   SER A 324 "
           pdb=" CA  SER A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.32   29.68     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 3051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 525
       0.068 -    0.135: 200
       0.135 -    0.203: 7
       0.203 -    0.270: 6
       0.270 -    0.338: 6
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CB  ILE D 360 "
            pdb=" CA  ILE D 360 "
            pdb=" CG1 ILE D 360 "
            pdb=" CG2 ILE D 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CB  ILE A 360 "
            pdb=" CA  ILE A 360 "
            pdb=" CG1 ILE A 360 "
            pdb=" CG2 ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" CB  ILE F 360 "
            pdb=" CA  ILE F 360 "
            pdb=" CG1 ILE F 360 "
            pdb=" CG2 ILE F 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 741 not shown)

  Planarity restraints: 846
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 331 "   -0.043 5.00e-02 4.00e+02   6.49e-02 6.75e+00
        pdb=" N   PRO D 332 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO D 332 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 332 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 331 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO E 332 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO E 332 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 332 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 331 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO A 332 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 843 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1238
        2.83 -     3.35: 3672
        3.35 -     3.86: 8108
        3.86 -     4.38: 8233
        4.38 -     4.90: 16275
  Nonbonded interactions: 37526
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 348 "
            pdb=" NZ  LYS B 347 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" OD2 ASP E 348 "
            pdb=" NZ  LYS F 347 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" N   ASP E 295 "
            pdb=" OD1 ASP E 295 "
     model   vdw
     2.393 3.120
  nonbonded pdb=" N   ASP C 295 "
            pdb=" OD1 ASP C 295 "
     model   vdw
     2.394 3.120
  nonbonded pdb=" N   ASP B 295 "
            pdb=" OD1 ASP B 295 "
     model   vdw
     2.394 3.120
  ... (remaining 37521 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             2.150
  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:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.360
  Find NCS groups from input model:        0.110
  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:13.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
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      :  0.011   0.094   4944  Z= 0.785
  Angle     :  1.098   9.474   6606  Z= 0.572
  Chirality :  0.068   0.338    744
  Planarity :  0.009   0.065    846
  Dihedral  :  9.926  41.614   1926
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.93 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.004   HIS C 329 
 PHE   0.009   0.003   PHE D 346 
 TYR   0.012   0.004   TYR E 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8612 (mttt) cc_final: 0.8312 (mtpm)
REVERT: A  369 LYS cc_start: 0.9012 (mttt) cc_final: 0.8731 (mttp)
REVERT: A  371 ILE cc_start: 0.8522 (mt) cc_final: 0.8241 (pp)
REVERT: B  343 LYS cc_start: 0.8711 (mttt) cc_final: 0.8468 (mtpm)
REVERT: C  343 LYS cc_start: 0.8639 (mttt) cc_final: 0.8280 (mtpp)
REVERT: D  343 LYS cc_start: 0.8718 (mttt) cc_final: 0.8439 (mtpp)
REVERT: D  360 ILE cc_start: 0.8497 (tt) cc_final: 0.7961 (mt)
REVERT: D  371 ILE cc_start: 0.8645 (mt) cc_final: 0.8293 (pp)
REVERT: E  343 LYS cc_start: 0.8866 (mttt) cc_final: 0.8610 (mtpm)
REVERT: F  279 ASN cc_start: 0.7680 (t0) cc_final: 0.7468 (t0)
REVERT: F  316 SER cc_start: 0.8797 (m) cc_final: 0.8514 (t)
REVERT: F  343 LYS cc_start: 0.8830 (mttt) cc_final: 0.8608 (mtpm)
REVERT: F  368 ASN cc_start: 0.7736 (m-40) cc_final: 0.7040 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.8984
  time to fit residues: 120.8733
Evaluate side-chains
  84 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 GLN
A 362 HIS
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
B 362 HIS
C 276 GLN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 362 HIS
** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 HIS
E 362 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.172844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.126928 restraints weight = 5159.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 2.39
r_work: 0.3997 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3883 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4944  Z= 0.241
  Angle     :  0.707  12.009   6606  Z= 0.344
  Chirality :  0.053   0.251    744
  Planarity :  0.005   0.038    846
  Dihedral  :  6.739  24.872    654
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 10.64 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.012   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.565 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8779 (mttt) cc_final: 0.8395 (mtpm)
REVERT: A  349 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7884 (mtp85)
REVERT: A  353 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8067 (tttm)
REVERT: A  371 ILE cc_start: 0.8676 (mt) cc_final: 0.8294 (pp)
REVERT: B  343 LYS cc_start: 0.8805 (mttt) cc_final: 0.8440 (mtpm)
REVERT: B  353 LYS cc_start: 0.8236 (ttpt) cc_final: 0.8021 (tttp)
REVERT: C  343 LYS cc_start: 0.8829 (mttt) cc_final: 0.8404 (mtpp)
REVERT: C  349 ARG cc_start: 0.8305 (mtt180) cc_final: 0.6914 (mmp-170)
REVERT: D  343 LYS cc_start: 0.8928 (mttt) cc_final: 0.8527 (mtpp)
REVERT: D  356 SER cc_start: 0.8815 (t) cc_final: 0.8554 (p)
REVERT: D  371 ILE cc_start: 0.8689 (mt) cc_final: 0.8279 (pp)
REVERT: E  343 LYS cc_start: 0.8979 (mttt) cc_final: 0.8597 (mtpm)
REVERT: E  351 GLN cc_start: 0.8240 (tt0) cc_final: 0.7746 (mt0)
REVERT: F  343 LYS cc_start: 0.8965 (mttt) cc_final: 0.8615 (mtpm)
REVERT: F  351 GLN cc_start: 0.8166 (tt0) cc_final: 0.7809 (mt0)
REVERT: F  368 ASN cc_start: 0.7799 (m-40) cc_final: 0.7182 (m110)
  outliers start: 17
  outliers final: 7
  residues processed: 101
  average time/residue: 0.8205
  time to fit residues: 87.6447
Evaluate side-chains
  79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  358 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 59 optimal weight:   30.0000
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.168707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.123176 restraints weight = 5418.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.44
r_work: 0.3931 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4944  Z= 0.294
  Angle     :  0.722  11.336   6606  Z= 0.348
  Chirality :  0.055   0.271    744
  Planarity :  0.004   0.032    846
  Dihedral  :  6.660  25.558    654
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 13.12 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.021   0.003   TYR E 310 
 ARG   0.001   0.000   ARG A 379 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8786 (mttt) cc_final: 0.8419 (mtpm)
REVERT: A  353 LYS cc_start: 0.8332 (ttpt) cc_final: 0.8110 (tttm)
REVERT: A  371 ILE cc_start: 0.8674 (mt) cc_final: 0.8269 (pp)
REVERT: B  343 LYS cc_start: 0.8788 (mttt) cc_final: 0.8412 (mtpm)
REVERT: B  353 LYS cc_start: 0.8277 (ttpt) cc_final: 0.8047 (tttm)
REVERT: C  274 LYS cc_start: 0.5912 (mtpt) cc_final: 0.4681 (pmtt)
REVERT: C  340 LYS cc_start: 0.8119 (mttt) cc_final: 0.7907 (mtpp)
REVERT: C  343 LYS cc_start: 0.8904 (mttt) cc_final: 0.8491 (mtpp)
REVERT: D  343 LYS cc_start: 0.8939 (mttt) cc_final: 0.8530 (mtpp)
REVERT: D  353 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8235 (tttp)
REVERT: D  356 SER cc_start: 0.8785 (t) cc_final: 0.8537 (p)
REVERT: D  371 ILE cc_start: 0.8605 (mt) cc_final: 0.8250 (pp)
REVERT: E  343 LYS cc_start: 0.8952 (mttt) cc_final: 0.8583 (mtpm)
REVERT: E  351 GLN cc_start: 0.8327 (tt0) cc_final: 0.7834 (mt0)
REVERT: F  343 LYS cc_start: 0.8937 (mttt) cc_final: 0.8582 (mtpm)
REVERT: F  351 GLN cc_start: 0.8154 (tt0) cc_final: 0.7813 (mt0)
REVERT: F  368 ASN cc_start: 0.7694 (m-40) cc_final: 0.7038 (m110)
  outliers start: 23
  outliers final: 14
  residues processed: 101
  average time/residue: 0.7769
  time to fit residues: 83.6097
Evaluate side-chains
  91 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 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 = 0.4543 r_free = 0.4543 target = 0.170323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.124932 restraints weight = 5400.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.38
r_work: 0.3928 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3810 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   4944  Z= 0.384
  Angle     :  0.750  10.373   6606  Z= 0.366
  Chirality :  0.055   0.205    744
  Planarity :  0.004   0.028    846
  Dihedral  :  6.914  26.304    654
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 14.01 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 362 
 PHE   0.007   0.002   PHE A 378 
 TYR   0.026   0.005   TYR E 310 
 ARG   0.002   0.000   ARG B 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8802 (mttt) cc_final: 0.8413 (mtpm)
REVERT: A  353 LYS cc_start: 0.8290 (ttpt) cc_final: 0.8017 (tttp)
REVERT: A  360 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7172 (mt)
REVERT: A  371 ILE cc_start: 0.8629 (mt) cc_final: 0.8197 (pp)
REVERT: B  343 LYS cc_start: 0.8776 (mttt) cc_final: 0.8389 (mtpm)
REVERT: B  353 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7935 (tttm)
REVERT: B  360 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7097 (mt)
REVERT: C  274 LYS cc_start: 0.5920 (mtpt) cc_final: 0.4924 (pmtt)
REVERT: C  340 LYS cc_start: 0.7977 (mttt) cc_final: 0.7724 (mtpp)
REVERT: C  343 LYS cc_start: 0.8868 (mttt) cc_final: 0.8451 (mtpp)
REVERT: D  274 LYS cc_start: 0.5840 (mtpt) cc_final: 0.5203 (pmtt)
REVERT: D  343 LYS cc_start: 0.8868 (mttt) cc_final: 0.8434 (mtpp)
REVERT: D  353 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8108 (tttp)
REVERT: D  356 SER cc_start: 0.8652 (t) cc_final: 0.8358 (p)
REVERT: D  358 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6813 (t70)
REVERT: D  371 ILE cc_start: 0.8592 (mt) cc_final: 0.8246 (pp)
REVERT: E  343 LYS cc_start: 0.8957 (mttt) cc_final: 0.8582 (mtpm)
REVERT: E  351 GLN cc_start: 0.8354 (tt0) cc_final: 0.7867 (mt0)
REVERT: E  360 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.6754 (mt)
REVERT: F  343 LYS cc_start: 0.8943 (mttt) cc_final: 0.8586 (mtpm)
REVERT: F  351 GLN cc_start: 0.8269 (tt0) cc_final: 0.7792 (mt0)
REVERT: F  368 ASN cc_start: 0.7620 (m-40) cc_final: 0.6933 (m110)
  outliers start: 27
  outliers final: 16
  residues processed: 99
  average time/residue: 0.8211
  time to fit residues: 86.0220
Evaluate side-chains
  93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** 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 = 0.4502 r_free = 0.4502 target = 0.165257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.119375 restraints weight = 5457.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 2.41
r_work: 0.3881 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   4944  Z= 0.396
  Angle     :  0.749  11.023   6606  Z= 0.364
  Chirality :  0.055   0.221    744
  Planarity :  0.003   0.026    846
  Dihedral  :  6.920  26.177    654
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 14.54 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 362 
 PHE   0.005   0.001   PHE C 346 
 TYR   0.029   0.005   TYR F 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8831 (mttt) cc_final: 0.8446 (mtpm)
REVERT: A  353 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8070 (tttp)
REVERT: A  360 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7094 (mt)
REVERT: A  368 ASN cc_start: 0.9088 (m-40) cc_final: 0.8627 (m-40)
REVERT: A  371 ILE cc_start: 0.8682 (mt) cc_final: 0.8264 (pp)
REVERT: B  343 LYS cc_start: 0.8823 (mttt) cc_final: 0.8443 (mtpm)
REVERT: B  353 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7963 (tttm)
REVERT: B  360 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.6892 (mt)
REVERT: C  340 LYS cc_start: 0.7988 (mttt) cc_final: 0.7783 (mtpp)
REVERT: C  343 LYS cc_start: 0.8916 (mttt) cc_final: 0.8505 (mtpp)
REVERT: D  274 LYS cc_start: 0.6184 (mtpt) cc_final: 0.5304 (pmtt)
REVERT: D  343 LYS cc_start: 0.8912 (mttt) cc_final: 0.8503 (mtpp)
REVERT: D  353 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8167 (tttp)
REVERT: D  358 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6602 (t70)
REVERT: D  360 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7925 (mt)
REVERT: D  371 ILE cc_start: 0.8765 (mt) cc_final: 0.8471 (pp)
REVERT: E  343 LYS cc_start: 0.9006 (mttt) cc_final: 0.8634 (mtpm)
REVERT: E  351 GLN cc_start: 0.8312 (tt0) cc_final: 0.7888 (mt0)
REVERT: F  343 LYS cc_start: 0.8970 (mttt) cc_final: 0.8625 (mtpm)
REVERT: F  351 GLN cc_start: 0.8286 (tt0) cc_final: 0.7845 (mt0)
REVERT: F  368 ASN cc_start: 0.7501 (m-40) cc_final: 0.6822 (m-40)
  outliers start: 30
  outliers final: 21
  residues processed: 96
  average time/residue: 0.7939
  time to fit residues: 80.9852
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    0.4980
   chunk 24 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** 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 = 0.4553 r_free = 0.4553 target = 0.169852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.124272 restraints weight = 5365.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 2.41
r_work: 0.3953 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4944  Z= 0.243
  Angle     :  0.688  11.263   6606  Z= 0.328
  Chirality :  0.053   0.206    744
  Planarity :  0.003   0.023    846
  Dihedral  :  6.360  24.829    654
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 14.54 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.027   0.004   TYR F 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 86
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8811 (mttt) cc_final: 0.8430 (mtpm)
REVERT: A  353 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8008 (tttp)
REVERT: A  368 ASN cc_start: 0.9113 (m-40) cc_final: 0.8634 (m-40)
REVERT: A  371 ILE cc_start: 0.8687 (mt) cc_final: 0.8289 (pp)
REVERT: B  343 LYS cc_start: 0.8804 (mttt) cc_final: 0.8413 (mtpm)
REVERT: B  353 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7871 (tttm)
REVERT: B  360 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.6983 (mt)
REVERT: B  371 ILE cc_start: 0.8853 (mt) cc_final: 0.8548 (pp)
REVERT: C  343 LYS cc_start: 0.8913 (mttt) cc_final: 0.8513 (mtpp)
REVERT: D  274 LYS cc_start: 0.6294 (mtpt) cc_final: 0.5175 (pmtt)
REVERT: D  343 LYS cc_start: 0.8910 (mttt) cc_final: 0.8495 (mtpp)
REVERT: D  353 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8124 (tttp)
REVERT: D  356 SER cc_start: 0.8862 (t) cc_final: 0.8591 (p)
REVERT: D  360 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8092 (mt)
REVERT: D  371 ILE cc_start: 0.8830 (mt) cc_final: 0.8590 (pp)
REVERT: E  343 LYS cc_start: 0.8971 (mttt) cc_final: 0.8603 (mtpm)
REVERT: E  351 GLN cc_start: 0.8298 (tt0) cc_final: 0.7892 (mt0)
REVERT: E  369 LYS cc_start: 0.4837 (pmtt) cc_final: 0.4616 (pmtt)
REVERT: F  274 LYS cc_start: 0.7039 (mtpt) cc_final: 0.6795 (ttpp)
REVERT: F  343 LYS cc_start: 0.8934 (mttt) cc_final: 0.8575 (mtpm)
REVERT: F  351 GLN cc_start: 0.8194 (tt0) cc_final: 0.7808 (mt0)
REVERT: F  368 ASN cc_start: 0.7532 (m-40) cc_final: 0.6878 (m-40)
  outliers start: 31
  outliers final: 20
  residues processed: 106
  average time/residue: 0.7492
  time to fit residues: 84.3647
Evaluate side-chains
  99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** 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 = 0.4540 r_free = 0.4540 target = 0.168961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.123155 restraints weight = 5277.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 2.39
r_work: 0.3937 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3818 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4944  Z= 0.264
  Angle     :  0.757  14.147   6606  Z= 0.348
  Chirality :  0.056   0.332    744
  Planarity :  0.003   0.025    846
  Dihedral  :  6.365  24.982    654
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 15.43 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.43 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.029   0.005   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8813 (mttt) cc_final: 0.8427 (mtpm)
REVERT: A  351 GLN cc_start: 0.7521 (tt0) cc_final: 0.7052 (mt0)
REVERT: A  353 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8116 (tttm)
REVERT: A  368 ASN cc_start: 0.9129 (m-40) cc_final: 0.8666 (m-40)
REVERT: A  371 ILE cc_start: 0.8670 (mt) cc_final: 0.8297 (pp)
REVERT: B  343 LYS cc_start: 0.8807 (mttt) cc_final: 0.8411 (mtpm)
REVERT: B  353 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7947 (tttm)
REVERT: B  360 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7055 (mt)
REVERT: B  371 ILE cc_start: 0.8815 (mt) cc_final: 0.8521 (pp)
REVERT: C  343 LYS cc_start: 0.8884 (mttt) cc_final: 0.8466 (mtpp)
REVERT: C  353 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8126 (tttp)
REVERT: C  360 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8054 (mt)
REVERT: D  274 LYS cc_start: 0.6400 (mtpt) cc_final: 0.5179 (pmtt)
REVERT: D  343 LYS cc_start: 0.8879 (mttt) cc_final: 0.8462 (mtpp)
REVERT: D  353 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8078 (tttp)
REVERT: D  356 SER cc_start: 0.8892 (t) cc_final: 0.8597 (p)
REVERT: D  358 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6487 (t0)
REVERT: D  360 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7985 (mt)
REVERT: D  371 ILE cc_start: 0.8817 (mt) cc_final: 0.8578 (pp)
REVERT: E  343 LYS cc_start: 0.8978 (mttt) cc_final: 0.8607 (mtpm)
REVERT: E  351 GLN cc_start: 0.8252 (tt0) cc_final: 0.7902 (mt0)
REVERT: F  274 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6873 (ttpp)
REVERT: F  343 LYS cc_start: 0.8929 (mttt) cc_final: 0.8571 (mtpm)
REVERT: F  351 GLN cc_start: 0.8313 (tt0) cc_final: 0.7867 (mt0)
REVERT: F  368 ASN cc_start: 0.7476 (m-40) cc_final: 0.6829 (m-40)
  outliers start: 29
  outliers final: 22
  residues processed: 105
  average time/residue: 0.7800
  time to fit residues: 86.9126
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0770
   chunk 41 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:   30.0000
   chunk 42 optimal weight:    5.9990
   overall best weight:    2.3344

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** 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 = 0.4541 r_free = 0.4541 target = 0.169186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.123288 restraints weight = 5368.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.41
r_work: 0.3940 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3822 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
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      :  0.004   0.035   4944  Z= 0.268
  Angle     :  0.736  13.001   6606  Z= 0.343
  Chirality :  0.056   0.276    744
  Planarity :  0.003   0.026    846
  Dihedral  :  6.334  24.757    654
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 17.20 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.031   0.006   TYR E 310 
 ARG   0.001   0.000   ARG B 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8814 (mttt) cc_final: 0.8433 (mtpm)
REVERT: A  351 GLN cc_start: 0.7527 (tt0) cc_final: 0.7070 (mt0)
REVERT: A  353 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8134 (tttp)
REVERT: A  368 ASN cc_start: 0.9134 (m-40) cc_final: 0.8638 (m-40)
REVERT: A  371 ILE cc_start: 0.8661 (mt) cc_final: 0.8313 (pp)
REVERT: B  343 LYS cc_start: 0.8799 (mttt) cc_final: 0.8404 (mtpm)
REVERT: B  353 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7961 (tttp)
REVERT: B  371 ILE cc_start: 0.8832 (mt) cc_final: 0.8533 (pp)
REVERT: C  343 LYS cc_start: 0.8878 (mttt) cc_final: 0.8488 (mtpp)
REVERT: C  353 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8119 (tttp)
REVERT: C  360 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8076 (mt)
REVERT: D  274 LYS cc_start: 0.6709 (mtpt) cc_final: 0.5381 (pmtt)
REVERT: D  343 LYS cc_start: 0.8879 (mttt) cc_final: 0.8466 (mtpp)
REVERT: D  353 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8098 (tttp)
REVERT: D  356 SER cc_start: 0.8910 (t) cc_final: 0.8618 (p)
REVERT: D  358 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6457 (t0)
REVERT: D  360 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7941 (mt)
REVERT: D  371 ILE cc_start: 0.8815 (mt) cc_final: 0.8584 (pp)
REVERT: E  343 LYS cc_start: 0.8967 (mttt) cc_final: 0.8603 (mtpm)
REVERT: E  351 GLN cc_start: 0.8149 (tt0) cc_final: 0.7857 (mt0)
REVERT: F  274 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6969 (ttpp)
REVERT: F  343 LYS cc_start: 0.8944 (mttt) cc_final: 0.8584 (mtpm)
REVERT: F  351 GLN cc_start: 0.8160 (tt0) cc_final: 0.7801 (mt0)
REVERT: F  368 ASN cc_start: 0.7664 (m-40) cc_final: 0.7096 (m-40)
  outliers start: 28
  outliers final: 22
  residues processed: 98
  average time/residue: 0.8974
  time to fit residues: 94.3135
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** 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 = 0.4609 r_free = 0.4609 target = 0.176518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.132031 restraints weight = 5230.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.4175 rms_B_bonded: 2.39
r_work: 0.4062 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3937 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4944  Z= 0.217
  Angle     :  0.727  12.766   6606  Z= 0.335
  Chirality :  0.055   0.261    744
  Planarity :  0.003   0.026    846
  Dihedral  :  6.113  24.315    654
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 17.91 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 362 
 PHE   0.003   0.001   PHE D 346 
 TYR   0.029   0.005   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8873 (mttt) cc_final: 0.8544 (mtpm)
REVERT: A  351 GLN cc_start: 0.7633 (tt0) cc_final: 0.7204 (mt0)
REVERT: A  353 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8228 (tttm)
REVERT: A  368 ASN cc_start: 0.9101 (m-40) cc_final: 0.8612 (m-40)
REVERT: A  371 ILE cc_start: 0.8772 (mt) cc_final: 0.8450 (pp)
REVERT: B  276 GLN cc_start: 0.7082 (mt0) cc_final: 0.6757 (mt0)
REVERT: B  343 LYS cc_start: 0.8867 (mttt) cc_final: 0.8532 (mtpm)
REVERT: B  353 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8117 (tttm)
REVERT: B  371 ILE cc_start: 0.8869 (mt) cc_final: 0.8552 (pp)
REVERT: C  343 LYS cc_start: 0.8928 (mttt) cc_final: 0.8552 (mtpp)
REVERT: C  353 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8213 (tttp)
REVERT: C  360 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8183 (mt)
REVERT: D  274 LYS cc_start: 0.6867 (mtpt) cc_final: 0.5467 (pmtt)
REVERT: D  343 LYS cc_start: 0.8948 (mttt) cc_final: 0.8565 (mtpp)
REVERT: D  356 SER cc_start: 0.9009 (t) cc_final: 0.8758 (p)
REVERT: D  358 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6289 (t0)
REVERT: D  360 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8091 (mt)
REVERT: E  343 LYS cc_start: 0.8959 (mttt) cc_final: 0.8635 (mtpm)
REVERT: E  351 GLN cc_start: 0.8160 (tt0) cc_final: 0.7931 (mt0)
REVERT: F  274 LYS cc_start: 0.7124 (mtpt) cc_final: 0.6889 (mtpp)
REVERT: F  343 LYS cc_start: 0.8909 (mttt) cc_final: 0.8605 (mtpm)
REVERT: F  351 GLN cc_start: 0.8096 (tt0) cc_final: 0.7833 (mt0)
REVERT: F  368 ASN cc_start: 0.8118 (m-40) cc_final: 0.7474 (m-40)
  outliers start: 29
  outliers final: 23
  residues processed: 105
  average time/residue: 0.9130
  time to fit residues: 101.5379
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 34 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0050
   overall best weight:    1.1600

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** 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 = 0.4623 r_free = 0.4623 target = 0.175151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.130378 restraints weight = 5259.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.4195 rms_B_bonded: 2.43
r_work: 0.4057 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3940 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4944  Z= 0.178
  Angle     :  0.719  12.623   6606  Z= 0.332
  Chirality :  0.054   0.267    744
  Planarity :  0.003   0.029    846
  Dihedral  :  5.895  23.466    654
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 19.50 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.42 (0.21), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 299 
 PHE   0.002   0.000   PHE E 346 
 TYR   0.029   0.006   TYR F 310 
 ARG   0.000   0.000   ARG E 349 

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8779 (mttt) cc_final: 0.8423 (mtpm)
REVERT: A  351 GLN cc_start: 0.7484 (tt0) cc_final: 0.7156 (mt0)
REVERT: A  353 LYS cc_start: 0.8381 (ttpt) cc_final: 0.8132 (tttm)
REVERT: A  368 ASN cc_start: 0.9094 (m-40) cc_final: 0.8586 (m-40)
REVERT: A  371 ILE cc_start: 0.8613 (mt) cc_final: 0.8312 (pp)
REVERT: B  340 LYS cc_start: 0.7980 (mttt) cc_final: 0.7769 (mtpp)
REVERT: B  343 LYS cc_start: 0.8791 (mttt) cc_final: 0.8421 (mtpm)
REVERT: B  353 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7997 (tttm)
REVERT: C  343 LYS cc_start: 0.8840 (mttt) cc_final: 0.8455 (mtpp)
REVERT: C  349 ARG cc_start: 0.8187 (mtt180) cc_final: 0.6772 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8117 (tttp)
REVERT: C  360 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8092 (mt)
REVERT: D  274 LYS cc_start: 0.6787 (mtpt) cc_final: 0.5421 (pmtt)
REVERT: D  343 LYS cc_start: 0.8871 (mttt) cc_final: 0.8461 (mtpp)
REVERT: D  349 ARG cc_start: 0.8096 (mtt180) cc_final: 0.6726 (mmp-170)
REVERT: D  356 SER cc_start: 0.8922 (t) cc_final: 0.8693 (p)
REVERT: D  360 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8146 (mt)
REVERT: E  325 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.6188 (pp)
REVERT: E  343 LYS cc_start: 0.8917 (mttt) cc_final: 0.8550 (mtpm)
REVERT: E  351 GLN cc_start: 0.8083 (tt0) cc_final: 0.7876 (mt0)
REVERT: F  274 LYS cc_start: 0.7098 (mtpt) cc_final: 0.6832 (ttpp)
REVERT: F  325 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.6128 (pp)
REVERT: F  343 LYS cc_start: 0.8857 (mttt) cc_final: 0.8507 (mtpm)
REVERT: F  351 GLN cc_start: 0.8034 (tt0) cc_final: 0.7798 (mt0)
REVERT: F  368 ASN cc_start: 0.8142 (m-40) cc_final: 0.7555 (m-40)
  outliers start: 26
  outliers final: 20
  residues processed: 100
  average time/residue: 0.8632
  time to fit residues: 91.1887
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 47 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 55 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 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 = 0.4595 r_free = 0.4595 target = 0.175319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.130313 restraints weight = 5264.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 2.40
r_work: 0.4019 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3903 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4944  Z= 0.258
  Angle     :  0.737  11.493   6606  Z= 0.346
  Chirality :  0.056   0.276    744
  Planarity :  0.003   0.027    846
  Dihedral  :  6.122  23.958    654
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 19.68 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.21), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.031   0.006   TYR E 310 
 ARG   0.001   0.000   ARG A 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4013.38 seconds
wall clock time: 72 minutes 25.02 seconds (4345.02 seconds total)