Starting phenix.real_space_refine
on Fri Aug 22 15:24:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tjx_10514/08_2025/6tjx_10514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tjx_10514/08_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_10514/08_2025/6tjx_10514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tjx_10514/08_2025/6tjx_10514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tjx_10514/08_2025/6tjx_10514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tjx_10514/08_2025/6tjx_10514.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.004
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D, E, F
  Time building chain proxies: 0.88, per 1000 atoms: 0.18
  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: 0.26
  Conformation dependent library (CDL) restraints added in 126.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.21
  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: 0.62

  Time building geometry restraints manager: 0.37 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             3.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.340
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.180
-------------------------------------------------------------------------------
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= 0.444
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG F 349 
 TYR   0.012   0.004   TYR E 310 
 PHE   0.009   0.003   PHE D 346 
 HIS   0.009   0.004   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.01149 ( 4944)
  covalent geometry    : angle       1.09784 ( 6606)
  hydrogen bonds       : bond        0.10362 (   68)
  hydrogen bonds       : angle       8.40137 (  204)

*********************** 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  : 0.150 
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: 0.3381
  time to fit residues: 45.4373
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  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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
F 362 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.177911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.132374 restraints weight = 5177.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 2.46
r_work: 0.4071 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3956 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4944  Z= 0.112
  Angle     :  0.680  11.900   6606  Z= 0.329
  Chirality :  0.052   0.234    744
  Planarity :  0.005   0.037    846
  Dihedral  :  6.465  24.048    654
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 10.28 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.68 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.011   0.002   TYR D 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4944)
  covalent geometry    : angle       0.67950 ( 6606)
  hydrogen bonds       : bond        0.01480 (   68)
  hydrogen bonds       : angle       5.23119 (  204)

*********************** 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
  116 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8695 (mttt) cc_final: 0.8276 (mtpm)
REVERT: A  349 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7905 (mtp85)
REVERT: A  371 ILE cc_start: 0.8676 (mt) cc_final: 0.8315 (pp)
REVERT: B  343 LYS cc_start: 0.8775 (mttt) cc_final: 0.8402 (mtpm)
REVERT: B  353 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7970 (tttm)
REVERT: C  291 CYS cc_start: 0.8773 (t) cc_final: 0.8266 (p)
REVERT: C  343 LYS cc_start: 0.8753 (mttt) cc_final: 0.8336 (mtpp)
REVERT: C  349 ARG cc_start: 0.8169 (mtt180) cc_final: 0.6865 (mmp-170)
REVERT: D  343 LYS cc_start: 0.8921 (mttt) cc_final: 0.8495 (mtpp)
REVERT: D  356 SER cc_start: 0.8873 (t) cc_final: 0.8627 (p)
REVERT: D  371 ILE cc_start: 0.8673 (mt) cc_final: 0.8275 (pp)
REVERT: E  343 LYS cc_start: 0.8939 (mttt) cc_final: 0.8547 (mtpm)
REVERT: E  349 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8197 (mtt180)
REVERT: F  343 LYS cc_start: 0.8948 (mttt) cc_final: 0.8590 (mtpm)
REVERT: F  351 GLN cc_start: 0.8158 (tt0) cc_final: 0.7808 (mt0)
REVERT: F  368 ASN cc_start: 0.7467 (m-40) cc_final: 0.6851 (m110)
  outliers start: 18
  outliers final: 5
  residues processed: 107
  average time/residue: 0.3455
  time to fit residues: 38.9375
Evaluate side-chains
  81 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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 E residue  358 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 9 optimal weight:   40.0000
   chunk 36 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0870
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.5964

-------------------------------------------------------------------------------
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
B 362 HIS
C 276 GLN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
E 351 GLN
F 362 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.173700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.128396 restraints weight = 5318.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 2.49
r_work: 0.4014 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3896 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4944  Z= 0.132
  Angle     :  0.688  11.572   6606  Z= 0.330
  Chirality :  0.054   0.274    744
  Planarity :  0.004   0.030    846
  Dihedral  :  6.300  24.795    654
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 13.83 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.55 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 379 
 TYR   0.022   0.004   TYR E 310 
 PHE   0.005   0.001   PHE E 346 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4944)
  covalent geometry    : angle       0.68793 ( 6606)
  hydrogen bonds       : bond        0.01258 (   68)
  hydrogen bonds       : angle       4.48533 (  204)

*********************** 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
  112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8761 (mttt) cc_final: 0.8366 (mtpm)
REVERT: A  353 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8076 (tttm)
REVERT: A  371 ILE cc_start: 0.8676 (mt) cc_final: 0.8245 (pp)
REVERT: A  379 ARG cc_start: 0.5710 (mmm-85) cc_final: 0.3792 (ptm160)
REVERT: B  343 LYS cc_start: 0.8751 (mttt) cc_final: 0.8377 (mtpm)
REVERT: B  353 LYS cc_start: 0.8278 (ttpt) cc_final: 0.8058 (tttm)
REVERT: C  343 LYS cc_start: 0.8885 (mttt) cc_final: 0.8479 (mtpp)
REVERT: C  349 ARG cc_start: 0.8206 (mtt180) cc_final: 0.6894 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8275 (tttp)
REVERT: D  343 LYS cc_start: 0.8949 (mttt) cc_final: 0.8556 (mtpp)
REVERT: D  353 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8262 (tttp)
REVERT: D  356 SER cc_start: 0.8836 (t) cc_final: 0.8603 (p)
REVERT: D  371 ILE cc_start: 0.8578 (mt) cc_final: 0.8217 (pp)
REVERT: E  325 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8032 (tm)
REVERT: E  343 LYS cc_start: 0.8921 (mttt) cc_final: 0.8544 (mtpm)
REVERT: E  351 GLN cc_start: 0.8244 (tt0) cc_final: 0.7800 (mt0)
REVERT: F  298 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8290 (mttt)
REVERT: F  343 LYS cc_start: 0.8898 (mttt) cc_final: 0.8540 (mtpm)
REVERT: F  351 GLN cc_start: 0.8116 (tt0) cc_final: 0.7812 (mt0)
REVERT: F  368 ASN cc_start: 0.7695 (m-40) cc_final: 0.7055 (m110)
  outliers start: 25
  outliers final: 14
  residues processed: 105
  average time/residue: 0.3707
  time to fit residues: 41.0541
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  320 SER
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  298 LYS
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 48 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 359 ASN
B 362 HIS
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.166618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.120861 restraints weight = 5379.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.37
r_work: 0.3866 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.068   4944  Z= 0.363
  Angle     :  0.849  12.515   6606  Z= 0.415
  Chirality :  0.060   0.324    744
  Planarity :  0.005   0.035    846
  Dihedral  :  7.422  27.075    654
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 15.25 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.73 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 349 
 TYR   0.027   0.005   TYR E 310 
 PHE   0.010   0.002   PHE C 346 
 HIS   0.006   0.002   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 ( 4944)
  covalent geometry    : angle       0.84889 ( 6606)
  hydrogen bonds       : bond        0.01526 (   68)
  hydrogen bonds       : angle       4.60253 (  204)

*********************** 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
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8788 (mttt) cc_final: 0.8405 (mtpm)
REVERT: A  353 LYS cc_start: 0.8293 (ttpt) cc_final: 0.8011 (tttm)
REVERT: A  360 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.6792 (mt)
REVERT: A  371 ILE cc_start: 0.8659 (mt) cc_final: 0.8236 (pp)
REVERT: B  343 LYS cc_start: 0.8787 (mttt) cc_final: 0.8399 (mtpm)
REVERT: B  353 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7938 (tttm)
REVERT: B  360 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.6854 (mt)
REVERT: C  274 LYS cc_start: 0.5890 (mtpt) cc_final: 0.4922 (pmtt)
REVERT: C  343 LYS cc_start: 0.8868 (mttt) cc_final: 0.8430 (mtpp)
REVERT: C  353 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8139 (tttp)
REVERT: C  360 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8141 (mt)
REVERT: D  274 LYS cc_start: 0.6003 (mtpt) cc_final: 0.5374 (pmtt)
REVERT: D  343 LYS cc_start: 0.8863 (mttt) cc_final: 0.8427 (mtpp)
REVERT: D  353 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8115 (tttp)
REVERT: D  358 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6648 (t0)
REVERT: D  360 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7981 (mt)
REVERT: E  343 LYS cc_start: 0.8950 (mttt) cc_final: 0.8591 (mtpm)
REVERT: F  343 LYS cc_start: 0.8943 (mttt) cc_final: 0.8580 (mtpm)
REVERT: F  351 GLN cc_start: 0.8348 (tt0) cc_final: 0.7827 (mt0)
REVERT: F  368 ASN cc_start: 0.7621 (m-40) cc_final: 0.6940 (m110)
  outliers start: 28
  outliers final: 19
  residues processed: 99
  average time/residue: 0.3764
  time to fit residues: 39.2817
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  291 CYS
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
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  320 SER
Chi-restraints excluded: chain E residue  325 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 59 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   chunk 35 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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**
** C 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 = 0.4570 r_free = 0.4570 target = 0.171197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.126004 restraints weight = 5377.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 2.42
r_work: 0.3983 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3867 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3858

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= 0.125
  Angle     :  0.688  12.579   6606  Z= 0.324
  Chirality :  0.053   0.177    744
  Planarity :  0.003   0.031    846
  Dihedral  :  6.339  24.524    654
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 17.38 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.56 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.021   0.004   TYR E 310 
 PHE   0.003   0.001   PHE D 346 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4944)
  covalent geometry    : angle       0.68777 ( 6606)
  hydrogen bonds       : bond        0.01249 (   68)
  hydrogen bonds       : angle       4.22989 (  204)

*********************** 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
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8796 (mttt) cc_final: 0.8414 (mtpm)
REVERT: A  353 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8025 (tttm)
REVERT: A  368 ASN cc_start: 0.9097 (m-40) cc_final: 0.8613 (m-40)
REVERT: A  371 ILE cc_start: 0.8682 (mt) cc_final: 0.8269 (pp)
REVERT: B  343 LYS cc_start: 0.8781 (mttt) cc_final: 0.8408 (mtpm)
REVERT: B  353 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7942 (tttm)
REVERT: C  274 LYS cc_start: 0.5976 (mtpt) cc_final: 0.4956 (pmtt)
REVERT: C  343 LYS cc_start: 0.8916 (mttt) cc_final: 0.8496 (mtpp)
REVERT: C  349 ARG cc_start: 0.8214 (mtt180) cc_final: 0.6980 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8230 (tttp)
REVERT: D  274 LYS cc_start: 0.5990 (mtpt) cc_final: 0.5396 (pmtt)
REVERT: D  343 LYS cc_start: 0.8913 (mttt) cc_final: 0.8499 (mtpp)
REVERT: D  353 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8217 (tttp)
REVERT: D  356 SER cc_start: 0.8841 (t) cc_final: 0.8596 (p)
REVERT: D  371 ILE cc_start: 0.8674 (mt) cc_final: 0.8374 (pp)
REVERT: E  325 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (tm)
REVERT: E  343 LYS cc_start: 0.8919 (mttt) cc_final: 0.8560 (mtpm)
REVERT: E  351 GLN cc_start: 0.8190 (tt0) cc_final: 0.7798 (mt0)
REVERT: F  274 LYS cc_start: 0.6894 (mtpt) cc_final: 0.6624 (ttpp)
REVERT: F  343 LYS cc_start: 0.8907 (mttt) cc_final: 0.8556 (mtpm)
REVERT: F  351 GLN cc_start: 0.8157 (tt0) cc_final: 0.7772 (mt0)
REVERT: F  368 ASN cc_start: 0.7628 (m-40) cc_final: 0.6989 (m-40)
  outliers start: 25
  outliers final: 17
  residues processed: 96
  average time/residue: 0.3912
  time to fit residues: 39.5228
Evaluate side-chains
  94 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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 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  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  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 4 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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**
** C 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 = 0.4542 r_free = 0.4542 target = 0.170632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.124811 restraints weight = 5467.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.41
r_work: 0.3929 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4944  Z= 0.227
  Angle     :  0.749  11.819   6606  Z= 0.356
  Chirality :  0.056   0.297    744
  Planarity :  0.003   0.032    846
  Dihedral  :  6.689  25.933    654
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 17.73 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG D 349 
 TYR   0.029   0.005   TYR F 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.004   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 4944)
  covalent geometry    : angle       0.74883 ( 6606)
  hydrogen bonds       : bond        0.01268 (   68)
  hydrogen bonds       : angle       4.15365 (  204)

*********************** 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
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8810 (mttt) cc_final: 0.8420 (mtpm)
REVERT: A  353 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8008 (tttm)
REVERT: A  368 ASN cc_start: 0.9114 (m-40) cc_final: 0.8616 (m-40)
REVERT: A  371 ILE cc_start: 0.8627 (mt) cc_final: 0.8213 (pp)
REVERT: B  343 LYS cc_start: 0.8808 (mttt) cc_final: 0.8415 (mtpm)
REVERT: B  353 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8037 (tttm)
REVERT: B  360 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7073 (mt)
REVERT: C  274 LYS cc_start: 0.5886 (mtpt) cc_final: 0.4820 (pmtt)
REVERT: C  343 LYS cc_start: 0.8883 (mttt) cc_final: 0.8465 (mtpp)
REVERT: C  353 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8084 (tttp)
REVERT: D  274 LYS cc_start: 0.6155 (mtpt) cc_final: 0.5254 (pmtt)
REVERT: D  343 LYS cc_start: 0.8856 (mttt) cc_final: 0.8437 (mtpp)
REVERT: D  353 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8094 (tttp)
REVERT: D  358 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6825 (t0)
REVERT: D  371 ILE cc_start: 0.8727 (mt) cc_final: 0.8440 (pp)
REVERT: E  343 LYS cc_start: 0.8919 (mttt) cc_final: 0.8568 (mtpm)
REVERT: E  351 GLN cc_start: 0.8307 (tt0) cc_final: 0.7887 (mt0)
REVERT: F  343 LYS cc_start: 0.8923 (mttt) cc_final: 0.8563 (mtpm)
REVERT: F  351 GLN cc_start: 0.8299 (tt0) cc_final: 0.7850 (mt0)
REVERT: F  368 ASN cc_start: 0.7559 (m-40) cc_final: 0.6901 (m-40)
  outliers start: 29
  outliers final: 19
  residues processed: 99
  average time/residue: 0.3533
  time to fit residues: 37.0379
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
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  325 LEU
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  360 ILE
Chi-restraints excluded: chain E residue  371 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 53 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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**
** C 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 = 0.4531 r_free = 0.4531 target = 0.167759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.121734 restraints weight = 5255.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.39
r_work: 0.3916 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3800 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.4038

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= 0.177
  Angle     :  0.719  11.945   6606  Z= 0.339
  Chirality :  0.055   0.256    744
  Planarity :  0.003   0.028    846
  Dihedral  :  6.438  25.208    654
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 17.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.52 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.025   0.004   TYR F 310 
 PHE   0.004   0.001   PHE D 346 
 HIS   0.003   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 4944)
  covalent geometry    : angle       0.71920 ( 6606)
  hydrogen bonds       : bond        0.01189 (   68)
  hydrogen bonds       : angle       3.98639 (  204)

*********************** 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
  111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8820 (mttt) cc_final: 0.8437 (mtpm)
REVERT: A  351 GLN cc_start: 0.7607 (tt0) cc_final: 0.7074 (mt0)
REVERT: A  353 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8053 (tttm)
REVERT: A  368 ASN cc_start: 0.9116 (m-40) cc_final: 0.8593 (m-40)
REVERT: A  371 ILE cc_start: 0.8658 (mt) cc_final: 0.8265 (pp)
REVERT: B  343 LYS cc_start: 0.8803 (mttt) cc_final: 0.8416 (mtpm)
REVERT: B  353 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7954 (tttm)
REVERT: B  360 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.6964 (mt)
REVERT: C  274 LYS cc_start: 0.5926 (mtpt) cc_final: 0.4841 (pmtt)
REVERT: C  343 LYS cc_start: 0.8919 (mttt) cc_final: 0.8510 (mtpp)
REVERT: C  353 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8108 (tttp)
REVERT: D  274 LYS cc_start: 0.6515 (mtpt) cc_final: 0.5308 (pmtt)
REVERT: D  343 LYS cc_start: 0.8885 (mttt) cc_final: 0.8476 (mtpp)
REVERT: D  353 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8131 (tttp)
REVERT: D  356 SER cc_start: 0.8899 (t) cc_final: 0.8604 (p)
REVERT: D  358 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6417 (t0)
REVERT: D  360 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7929 (mt)
REVERT: D  371 ILE cc_start: 0.8819 (mt) cc_final: 0.8571 (pp)
REVERT: E  343 LYS cc_start: 0.8949 (mttt) cc_final: 0.8594 (mtpm)
REVERT: E  351 GLN cc_start: 0.8305 (tt0) cc_final: 0.7900 (mt0)
REVERT: F  343 LYS cc_start: 0.8928 (mttt) cc_final: 0.8576 (mtpm)
REVERT: F  351 GLN cc_start: 0.8211 (tt0) cc_final: 0.7833 (mt0)
REVERT: F  368 ASN cc_start: 0.7569 (m-40) cc_final: 0.6925 (m-40)
  outliers start: 29
  outliers final: 21
  residues processed: 101
  average time/residue: 0.3164
  time to fit residues: 33.8387
Evaluate side-chains
  99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
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 D residue  320 SER
Chi-restraints excluded: chain D residue  352 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  320 SER
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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**
** C 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 = 0.4580 r_free = 0.4580 target = 0.171766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.125896 restraints weight = 5273.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.4131 rms_B_bonded: 2.43
r_work: 0.3979 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3861 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4944  Z= 0.134
  Angle     :  0.718  13.165   6606  Z= 0.332
  Chirality :  0.056   0.331    744
  Planarity :  0.003   0.029    846
  Dihedral  :  6.098  24.254    654
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.44 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.41 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.028   0.005   TYR F 310 
 PHE   0.003   0.001   PHE C 346 
 HIS   0.002   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4944)
  covalent geometry    : angle       0.71763 ( 6606)
  hydrogen bonds       : bond        0.01123 (   68)
  hydrogen bonds       : angle       3.77992 (  204)

*********************** 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
  112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8795 (mttt) cc_final: 0.8418 (mtpm)
REVERT: A  351 GLN cc_start: 0.7512 (tt0) cc_final: 0.7073 (mt0)
REVERT: A  353 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8105 (tttm)
REVERT: A  368 ASN cc_start: 0.9138 (m-40) cc_final: 0.8633 (m-40)
REVERT: A  371 ILE cc_start: 0.8706 (mt) cc_final: 0.8356 (pp)
REVERT: B  343 LYS cc_start: 0.8780 (mttt) cc_final: 0.8395 (mtpm)
REVERT: B  353 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7962 (tttp)
REVERT: B  360 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7190 (mt)
REVERT: B  371 ILE cc_start: 0.8835 (mt) cc_final: 0.8521 (pp)
REVERT: C  274 LYS cc_start: 0.5957 (mtpt) cc_final: 0.4847 (pmtt)
REVERT: C  343 LYS cc_start: 0.8903 (mttt) cc_final: 0.8507 (mtpp)
REVERT: C  349 ARG cc_start: 0.8265 (mtt180) cc_final: 0.6847 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8106 (tttp)
REVERT: D  274 LYS cc_start: 0.6659 (mtpt) cc_final: 0.5409 (pmtt)
REVERT: D  343 LYS cc_start: 0.8873 (mttt) cc_final: 0.8466 (mtpp)
REVERT: D  353 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8122 (tttp)
REVERT: D  356 SER cc_start: 0.8932 (t) cc_final: 0.8689 (p)
REVERT: D  358 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6674 (t0)
REVERT: D  371 ILE cc_start: 0.8805 (mt) cc_final: 0.8587 (pp)
REVERT: E  343 LYS cc_start: 0.8924 (mttt) cc_final: 0.8566 (mtpm)
REVERT: E  351 GLN cc_start: 0.8180 (tt0) cc_final: 0.7897 (mt0)
REVERT: F  274 LYS cc_start: 0.7052 (mtpt) cc_final: 0.6807 (ttpp)
REVERT: F  343 LYS cc_start: 0.8924 (mttt) cc_final: 0.8558 (mtpm)
REVERT: F  351 GLN cc_start: 0.8081 (tt0) cc_final: 0.7746 (mt0)
REVERT: F  368 ASN cc_start: 0.7542 (m-40) cc_final: 0.6971 (m-40)
  outliers start: 25
  outliers final: 22
  residues processed: 103
  average time/residue: 0.3449
  time to fit residues: 37.4508
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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  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  352 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  291 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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**
** C 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 = 0.4675 r_free = 0.4675 target = 0.180012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.135412 restraints weight = 5168.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.4270 rms_B_bonded: 2.49
r_work: 0.4122 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4001 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4944  Z= 0.094
  Angle     :  0.679  12.250   6606  Z= 0.317
  Chirality :  0.054   0.255    744
  Planarity :  0.003   0.030    846
  Dihedral  :  5.626  22.940    654
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.68 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 349 
 TYR   0.027   0.005   TYR F 310 
 PHE   0.002   0.000   PHE F 378 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 4944)
  covalent geometry    : angle       0.67854 ( 6606)
  hydrogen bonds       : bond        0.01119 (   68)
  hydrogen bonds       : angle       3.57269 (  204)

*********************** 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
  120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8764 (mttt) cc_final: 0.8401 (mtpm)
REVERT: A  351 GLN cc_start: 0.7460 (tt0) cc_final: 0.7150 (mt0)
REVERT: A  353 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8091 (tttm)
REVERT: A  368 ASN cc_start: 0.9159 (m-40) cc_final: 0.8652 (m-40)
REVERT: A  371 ILE cc_start: 0.8661 (mt) cc_final: 0.8342 (pp)
REVERT: B  274 LYS cc_start: 0.5985 (mtpt) cc_final: 0.5724 (ttpp)
REVERT: B  343 LYS cc_start: 0.8774 (mttt) cc_final: 0.8387 (mtpm)
REVERT: B  349 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7741 (mtt180)
REVERT: B  353 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7978 (tttp)
REVERT: B  371 ILE cc_start: 0.8819 (mt) cc_final: 0.8521 (pp)
REVERT: C  274 LYS cc_start: 0.5965 (mtpt) cc_final: 0.4681 (pmtt)
REVERT: C  343 LYS cc_start: 0.8844 (mttt) cc_final: 0.8431 (mtpp)
REVERT: C  349 ARG cc_start: 0.8181 (mtt180) cc_final: 0.6747 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8141 (tttp)
REVERT: D  274 LYS cc_start: 0.6581 (mtpt) cc_final: 0.5337 (pmtt)
REVERT: D  343 LYS cc_start: 0.8866 (mttt) cc_final: 0.8464 (mtpp)
REVERT: D  349 ARG cc_start: 0.8134 (mtt180) cc_final: 0.6740 (mmp-170)
REVERT: D  353 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8135 (tttp)
REVERT: E  325 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.5995 (pt)
REVERT: E  343 LYS cc_start: 0.8819 (mttt) cc_final: 0.8440 (mtpm)
REVERT: E  351 GLN cc_start: 0.8077 (tt0) cc_final: 0.7875 (mt0)
REVERT: F  274 LYS cc_start: 0.7179 (mtpt) cc_final: 0.6853 (ttpp)
REVERT: F  325 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6119 (pt)
REVERT: F  343 LYS cc_start: 0.8854 (mttt) cc_final: 0.8467 (mtpm)
REVERT: F  351 GLN cc_start: 0.8020 (tt0) cc_final: 0.7758 (mt0)
REVERT: F  368 ASN cc_start: 0.7975 (m-40) cc_final: 0.7372 (m-40)
  outliers start: 23
  outliers final: 20
  residues processed: 110
  average time/residue: 0.3727
  time to fit residues: 43.1383
Evaluate side-chains
  115 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
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 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 D residue  352 SER
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  320 SER
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 15 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 40 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   overall best weight:    2.0200

-------------------------------------------------------------------------------
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**
** C 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 = 0.4600 r_free = 0.4600 target = 0.173091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.126687 restraints weight = 5336.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 2.49
r_work: 0.3993 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3873 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4944  Z= 0.156
  Angle     :  0.704  11.403   6606  Z= 0.336
  Chirality :  0.056   0.283    744
  Planarity :  0.004   0.029    846
  Dihedral  :  5.978  23.171    654
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 19.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.21), residues: 630

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4944)
  covalent geometry    : angle       0.70434 ( 6606)
  hydrogen bonds       : bond        0.01090 (   68)
  hydrogen bonds       : angle       3.65190 (  204)

********************** 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
  113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8786 (mttt) cc_final: 0.8425 (mtpm)
REVERT: A  351 GLN cc_start: 0.7490 (tt0) cc_final: 0.7132 (mt0)
REVERT: A  353 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8160 (tttm)
REVERT: A  368 ASN cc_start: 0.9150 (m-40) cc_final: 0.8662 (m-40)
REVERT: A  371 ILE cc_start: 0.8672 (mt) cc_final: 0.8341 (pp)
REVERT: B  274 LYS cc_start: 0.6194 (mtpt) cc_final: 0.5886 (ttpp)
REVERT: B  343 LYS cc_start: 0.8787 (mttt) cc_final: 0.8398 (mtpm)
REVERT: B  353 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8066 (tttm)
REVERT: B  360 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7318 (mt)
REVERT: C  274 LYS cc_start: 0.6054 (mtpt) cc_final: 0.4717 (pmtt)
REVERT: C  343 LYS cc_start: 0.8814 (mttt) cc_final: 0.8417 (mtpp)
REVERT: C  349 ARG cc_start: 0.8261 (mtt180) cc_final: 0.6839 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8116 (tttp)
REVERT: D  274 LYS cc_start: 0.6711 (mtpt) cc_final: 0.5371 (pmtt)
REVERT: D  343 LYS cc_start: 0.8820 (mttt) cc_final: 0.8423 (mtpp)
REVERT: D  353 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8109 (tttp)
REVERT: D  358 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6688 (t0)
REVERT: E  325 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.6139 (pt)
REVERT: E  343 LYS cc_start: 0.8862 (mttt) cc_final: 0.8522 (mtpm)
REVERT: F  274 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6731 (ttpp)
REVERT: F  325 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.6198 (pt)
REVERT: F  343 LYS cc_start: 0.8896 (mttt) cc_final: 0.8532 (mtpm)
REVERT: F  351 GLN cc_start: 0.8056 (tt0) cc_final: 0.7799 (mt0)
REVERT: F  368 ASN cc_start: 0.7983 (m-40) cc_final: 0.7386 (m-40)
  outliers start: 28
  outliers final: 20
  residues processed: 103
  average time/residue: 0.3705
  time to fit residues: 40.3268
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
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  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  352 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  320 SER
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 45 optimal weight:    0.0060
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0470
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.4094

-------------------------------------------------------------------------------
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**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 351 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.184342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.140345 restraints weight = 5139.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4342 rms_B_bonded: 2.49
r_work: 0.4198 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4076 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4944  Z= 0.091
  Angle     :  0.671  11.133   6606  Z= 0.319
  Chirality :  0.053   0.258    744
  Planarity :  0.004   0.034    846
  Dihedral  :  5.434  21.956    654
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.10 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.12 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.21), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.025   0.005   TYR F 310 
 PHE   0.002   0.000   PHE F 378 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 4944)
  covalent geometry    : angle       0.67052 ( 6606)
  hydrogen bonds       : bond        0.01089 (   68)
  hydrogen bonds       : angle       3.43993 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1838.10 seconds
wall clock time: 32 minutes 5.32 seconds (1925.32 seconds total)