Starting phenix.real_space_refine
on Thu Mar  6 04:39:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tjx_10514/03_2025/6tjx_10514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tjx_10514/03_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_10514/03_2025/6tjx_10514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tjx_10514/03_2025/6tjx_10514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tjx_10514/03_2025/6tjx_10514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tjx_10514/03_2025/6tjx_10514.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    3042      2.51       5
     N     906      2.21       5
     O     918      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4878
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 5.89, per 1000 atoms: 1.21
  Number of scatterers: 4878
  At special positions: 0
  Unit cell: (180.55, 141.45, 32.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     918      8.00
     N     906      7.00
     C    3042      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 770.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 30.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 279
      removed outlier: 6.280A  pdb=" N   GLN A 276 " --> pdb=" O   ILE E 277 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   ASN E 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   ILE A 278 " --> pdb=" O   ASN E 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 286 through 289
      removed outlier: 6.204A  pdb=" N   VAL A 287 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.427A  pdb=" N   VAL A 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   VAL C 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 318 through 319
      removed outlier: 6.663A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 327 through 330
      removed outlier: 6.823A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 339
      removed outlier: 6.259A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.519A  pdb=" N   ASP A 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.208A  pdb=" N   VAL A 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   LYS C 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   SER A 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.659A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 377
      removed outlier: 6.597A  pdb=" N   LYS A 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   THR C 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   GLU A 372 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LYS C 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   HIS A 374 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   THR C 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU A 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 275 through 279
      removed outlier: 6.240A  pdb=" N   GLN B 276 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ASN F 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   ILE B 278 " --> pdb=" O   ASN F 279 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 286 through 289
      removed outlier: 6.191A  pdb=" N   VAL B 287 " --> pdb=" O   GLN D 288 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.382A  pdb=" N   VAL B 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   VAL D 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 318 through 319
      removed outlier: 6.645A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 327 through 330
      removed outlier: 6.825A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 336 through 339
      removed outlier: 6.294A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 345 through 346
      removed outlier: 6.514A  pdb=" N   ASP B 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 350 through 354
      removed outlier: 6.231A  pdb=" N   VAL B 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   LYS D 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER B 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 360 through 362
    Processing sheet with id=AC2, first strand: chain 'D' and resid 369 through 377
      removed outlier: 6.684A  pdb=" N   LYS B 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   THR D 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   GLU B 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   LYS D 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   HIS B 374 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   THR D 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.43 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             107.480
  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:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.890
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:22.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  152.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.094   4944  Z= 0.785
  Angle     :  1.098   9.474   6606  Z= 0.572
  Chirality :  0.068   0.338    744
  Planarity :  0.009   0.065    846
  Dihedral  :  9.926  41.614   1926
  Min Nonbonded Distance : 2.312

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

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

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

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.614 
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: 1.0617
  time to fit residues: 143.0284
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  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.7988

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.172844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.126924 restraints weight = 5159.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 2.39
r_work: 0.3996 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3881 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2538

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

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

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

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

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8778 (mttt) cc_final: 0.8394 (mtpm)
REVERT: A  349 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7875 (mtp85)
REVERT: A  353 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8066 (tttm)
REVERT: A  371 ILE cc_start: 0.8658 (mt) cc_final: 0.8274 (pp)
REVERT: B  343 LYS cc_start: 0.8802 (mttt) cc_final: 0.8438 (mtpm)
REVERT: B  353 LYS cc_start: 0.8235 (ttpt) cc_final: 0.8018 (tttp)
REVERT: C  343 LYS cc_start: 0.8830 (mttt) cc_final: 0.8405 (mtpp)
REVERT: C  349 ARG cc_start: 0.8296 (mtt180) cc_final: 0.6908 (mmp-170)
REVERT: D  343 LYS cc_start: 0.8927 (mttt) cc_final: 0.8526 (mtpp)
REVERT: D  356 SER cc_start: 0.8812 (t) cc_final: 0.8550 (p)
REVERT: D  371 ILE cc_start: 0.8669 (mt) cc_final: 0.8256 (pp)
REVERT: E  343 LYS cc_start: 0.8977 (mttt) cc_final: 0.8596 (mtpm)
REVERT: E  351 GLN cc_start: 0.8241 (tt0) cc_final: 0.7745 (mt0)
REVERT: F  343 LYS cc_start: 0.8962 (mttt) cc_final: 0.8612 (mtpm)
REVERT: F  351 GLN cc_start: 0.8169 (tt0) cc_final: 0.7809 (mt0)
REVERT: F  368 ASN cc_start: 0.7806 (m-40) cc_final: 0.7188 (m110)
  outliers start: 17
  outliers final: 7
  residues processed: 101
  average time/residue: 0.9157
  time to fit residues: 98.2395
Evaluate side-chains
  79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  358 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:   30.0000
   chunk 56 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    3.3988

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.170014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.124853 restraints weight = 5410.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 2.41
r_work: 0.3923 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3807 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   4944  Z= 0.372
  Angle     :  0.754  11.611   6606  Z= 0.366
  Chirality :  0.056   0.275    744
  Planarity :  0.004   0.031    846
  Dihedral  :  6.937  26.473    654
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 13.12 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 362 
 PHE   0.007   0.002   PHE B 346 
 TYR   0.022   0.003   TYR E 310 
 ARG   0.002   0.000   ARG A 379 

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8772 (mttt) cc_final: 0.8388 (mtpm)
REVERT: A  353 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8056 (tttp)
REVERT: A  368 ASN cc_start: 0.9130 (m-40) cc_final: 0.8886 (m-40)
REVERT: A  371 ILE cc_start: 0.8678 (mt) cc_final: 0.8271 (pp)
REVERT: B  343 LYS cc_start: 0.8770 (mttt) cc_final: 0.8389 (mtpm)
REVERT: B  353 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7984 (tttm)
REVERT: B  360 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.6944 (mt)
REVERT: C  274 LYS cc_start: 0.5898 (mtpt) cc_final: 0.4901 (pmtt)
REVERT: C  343 LYS cc_start: 0.8861 (mttt) cc_final: 0.8437 (mtpp)
REVERT: D  343 LYS cc_start: 0.8871 (mttt) cc_final: 0.8429 (mtpp)
REVERT: D  353 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8183 (tttp)
REVERT: D  356 SER cc_start: 0.8740 (t) cc_final: 0.8452 (p)
REVERT: E  343 LYS cc_start: 0.8944 (mttt) cc_final: 0.8568 (mtpm)
REVERT: E  351 GLN cc_start: 0.8401 (tt0) cc_final: 0.7843 (mt0)
REVERT: F  343 LYS cc_start: 0.8934 (mttt) cc_final: 0.8572 (mtpm)
REVERT: F  351 GLN cc_start: 0.8211 (tt0) cc_final: 0.7801 (mt0)
REVERT: F  368 ASN cc_start: 0.7665 (m-40) cc_final: 0.6978 (m110)
  outliers start: 24
  outliers final: 15
  residues processed: 102
  average time/residue: 0.7628
  time to fit residues: 82.4536
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  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain 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 D residue  320 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0980
   chunk 19 optimal weight:   30.0000
   chunk 42 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.5986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.172491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.127440 restraints weight = 5345.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 2.43
r_work: 0.4004 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3886 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3635

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= 0.205
  Angle     :  0.672  11.072   6606  Z= 0.322
  Chirality :  0.052   0.193    744
  Planarity :  0.003   0.026    846
  Dihedral  :  6.216  24.610    654
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 13.83 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.025   0.004   TYR F 310 
 ARG   0.001   0.000   ARG A 379 

*********************** 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
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.8801 (mttt) cc_final: 0.8425 (mtpm)
REVERT: A  353 LYS cc_start: 0.8259 (ttpt) cc_final: 0.8033 (tttp)
REVERT: A  368 ASN cc_start: 0.9173 (m-40) cc_final: 0.8926 (m-40)
REVERT: A  371 ILE cc_start: 0.8683 (mt) cc_final: 0.8265 (pp)
REVERT: A  379 ARG cc_start: 0.5792 (mmm-85) cc_final: 0.5133 (mmt90)
REVERT: B  343 LYS cc_start: 0.8788 (mttt) cc_final: 0.8408 (mtpm)
REVERT: B  353 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7957 (tttm)
REVERT: C  274 LYS cc_start: 0.5920 (mtpt) cc_final: 0.4811 (pmtt)
REVERT: C  343 LYS cc_start: 0.8921 (mttt) cc_final: 0.8496 (mtpp)
REVERT: C  349 ARG cc_start: 0.8210 (mtt180) cc_final: 0.6897 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8243 (tttp)
REVERT: D  343 LYS cc_start: 0.8914 (mttt) cc_final: 0.8478 (mtpp)
REVERT: D  353 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8211 (tttp)
REVERT: D  356 SER cc_start: 0.8796 (t) cc_final: 0.8580 (p)
REVERT: D  371 ILE cc_start: 0.8605 (mt) cc_final: 0.8281 (pp)
REVERT: E  343 LYS cc_start: 0.8941 (mttt) cc_final: 0.8566 (mtpm)
REVERT: E  351 GLN cc_start: 0.8232 (tt0) cc_final: 0.7829 (mt0)
REVERT: F  343 LYS cc_start: 0.8911 (mttt) cc_final: 0.8549 (mtpm)
REVERT: F  351 GLN cc_start: 0.8182 (tt0) cc_final: 0.7809 (mt0)
REVERT: F  368 ASN cc_start: 0.7661 (m-40) cc_final: 0.7003 (m110)
  outliers start: 27
  outliers final: 18
  residues processed: 99
  average time/residue: 0.7917
  time to fit residues: 83.6069
Evaluate side-chains
  93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
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  358 ASP
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 9 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    6.9990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.159200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.113128 restraints weight = 5590.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.35
r_work: 0.3794 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.080   4944  Z= 0.694
  Angle     :  0.906  13.804   6606  Z= 0.441
  Chirality :  0.062   0.341    744
  Planarity :  0.004   0.028    846
  Dihedral  :  7.667  28.038    654
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 14.36 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.79 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS A 362 
 PHE   0.009   0.002   PHE E 346 
 TYR   0.031   0.006   TYR F 310 
 ARG   0.003   0.001   ARG B 349 

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8869 (mttt) cc_final: 0.8495 (mtpm)
REVERT: A  353 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8122 (tttp)
REVERT: A  360 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7098 (mt)
REVERT: A  368 ASN cc_start: 0.9157 (m-40) cc_final: 0.8923 (m-40)
REVERT: A  371 ILE cc_start: 0.8713 (mt) cc_final: 0.8253 (pp)
REVERT: B  343 LYS cc_start: 0.8855 (mttt) cc_final: 0.8476 (mtpm)
REVERT: B  353 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8140 (tttm)
REVERT: B  360 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.6995 (mt)
REVERT: C  343 LYS cc_start: 0.8941 (mttt) cc_final: 0.8526 (mtpp)
REVERT: C  353 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8154 (tttp)
REVERT: D  274 LYS cc_start: 0.6497 (mtpt) cc_final: 0.5516 (pmtt)
REVERT: D  343 LYS cc_start: 0.8922 (mttt) cc_final: 0.8492 (mtpp)
REVERT: D  353 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8172 (tttp)
REVERT: D  358 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6809 (t70)
REVERT: D  360 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7922 (mt)
REVERT: E  343 LYS cc_start: 0.9024 (mttt) cc_final: 0.8664 (mtpm)
REVERT: E  369 LYS cc_start: 0.5003 (pmtt) cc_final: 0.4610 (pptt)
REVERT: F  343 LYS cc_start: 0.8994 (mttt) cc_final: 0.8650 (mtpm)
REVERT: F  351 GLN cc_start: 0.8293 (tt0) cc_final: 0.7816 (mt0)
REVERT: F  368 ASN cc_start: 0.7802 (m-40) cc_final: 0.7111 (m110)
  outliers start: 30
  outliers final: 21
  residues processed: 95
  average time/residue: 0.8068
  time to fit residues: 81.2275
Evaluate side-chains
  95 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
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  295 ASP
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  358 ASP
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.9582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.173090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.128804 restraints weight = 5339.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.40
r_work: 0.4020 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3902 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4944  Z= 0.163
  Angle     :  0.705  12.070   6606  Z= 0.325
  Chirality :  0.055   0.313    744
  Planarity :  0.003   0.021    846
  Dihedral  :  6.171  23.541    654
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 16.31 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.51 (0.25), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.003   0.001   PHE D 346 
 TYR   0.023   0.004   TYR F 310 
 ARG   0.001   0.000   ARG F 349 

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8813 (mttt) cc_final: 0.8438 (mtpm)
REVERT: A  353 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7909 (tttm)
REVERT: A  368 ASN cc_start: 0.9211 (m-40) cc_final: 0.9003 (m110)
REVERT: A  371 ILE cc_start: 0.8676 (mt) cc_final: 0.8271 (pp)
REVERT: B  343 LYS cc_start: 0.8792 (mttt) cc_final: 0.8404 (mtpm)
REVERT: B  353 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7882 (tttp)
REVERT: C  343 LYS cc_start: 0.8940 (mttt) cc_final: 0.8527 (mtpp)
REVERT: C  349 ARG cc_start: 0.8141 (mtt180) cc_final: 0.6822 (mmp-170)
REVERT: D  343 LYS cc_start: 0.8919 (mttt) cc_final: 0.8497 (mtpp)
REVERT: D  349 ARG cc_start: 0.8102 (mtt180) cc_final: 0.6897 (mmp-170)
REVERT: D  353 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8096 (tttp)
REVERT: D  356 SER cc_start: 0.8949 (t) cc_final: 0.8686 (p)
REVERT: D  371 ILE cc_start: 0.8792 (mt) cc_final: 0.8514 (pp)
REVERT: E  343 LYS cc_start: 0.8944 (mttt) cc_final: 0.8581 (mtpm)
REVERT: E  351 GLN cc_start: 0.8295 (tt0) cc_final: 0.7862 (mt0)
REVERT: E  369 LYS cc_start: 0.4912 (pmtt) cc_final: 0.4537 (pptt)
REVERT: F  274 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6747 (ttpp)
REVERT: F  343 LYS cc_start: 0.8909 (mttt) cc_final: 0.8546 (mtpm)
REVERT: F  351 GLN cc_start: 0.8187 (tt0) cc_final: 0.7779 (mt0)
REVERT: F  368 ASN cc_start: 0.7601 (m-40) cc_final: 0.6937 (m-40)
  outliers start: 25
  outliers final: 20
  residues processed: 99
  average time/residue: 0.9777
  time to fit residues: 102.6918
Evaluate side-chains
  97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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  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 C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain D residue  358 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    0.0270
   chunk 56 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0670
   chunk 41 optimal weight:   10.0000
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5176

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.182212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.138762 restraints weight = 5186.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4301 rms_B_bonded: 2.46
r_work: 0.4163 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.4045 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.4366

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= 0.136
  Angle     :  0.680  11.397   6606  Z= 0.312
  Chirality :  0.054   0.254    744
  Planarity :  0.003   0.023    846
  Dihedral  :  5.603  22.912    654
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.26 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.002   0.000   PHE F 378 
 TYR   0.023   0.005   TYR E 310 
 ARG   0.001   0.000   ARG C 379 

*********************** 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
  118 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8763 (mttt) cc_final: 0.8392 (mtpm)
REVERT: A  351 GLN cc_start: 0.7455 (tt0) cc_final: 0.7135 (mt0)
REVERT: A  353 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7891 (tttm)
REVERT: A  368 ASN cc_start: 0.9211 (m-40) cc_final: 0.9004 (m110)
REVERT: A  371 ILE cc_start: 0.8776 (mt) cc_final: 0.8406 (pp)
REVERT: B  340 LYS cc_start: 0.7966 (mttt) cc_final: 0.7753 (mtpp)
REVERT: B  343 LYS cc_start: 0.8780 (mttt) cc_final: 0.8409 (mtpm)
REVERT: B  353 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7925 (tttm)
REVERT: B  371 ILE cc_start: 0.8809 (mt) cc_final: 0.8515 (pp)
REVERT: C  274 LYS cc_start: 0.6061 (mtpt) cc_final: 0.4970 (pmtt)
REVERT: C  343 LYS cc_start: 0.8889 (mttt) cc_final: 0.8494 (mtpp)
REVERT: C  349 ARG cc_start: 0.8179 (mtt180) cc_final: 0.6579 (mmp-170)
REVERT: D  343 LYS cc_start: 0.8902 (mttt) cc_final: 0.8492 (mtpp)
REVERT: D  349 ARG cc_start: 0.8143 (mtt180) cc_final: 0.6759 (mmp-170)
REVERT: D  353 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8180 (tttp)
REVERT: D  356 SER cc_start: 0.8880 (t) cc_final: 0.8675 (p)
REVERT: D  371 ILE cc_start: 0.8730 (mt) cc_final: 0.8525 (pp)
REVERT: E  343 LYS cc_start: 0.8797 (mttt) cc_final: 0.8433 (mtpm)
REVERT: E  351 GLN cc_start: 0.8129 (tt0) cc_final: 0.7857 (mt0)
REVERT: F  295 ASP cc_start: 0.8422 (p0) cc_final: 0.8183 (p0)
REVERT: F  325 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6063 (pt)
REVERT: F  343 LYS cc_start: 0.8787 (mttt) cc_final: 0.8410 (mtpm)
REVERT: F  351 GLN cc_start: 0.8024 (tt0) cc_final: 0.7718 (mt0)
REVERT: F  368 ASN cc_start: 0.7571 (m-40) cc_final: 0.6989 (m-40)
  outliers start: 21
  outliers final: 15
  residues processed: 110
  average time/residue: 0.7906
  time to fit residues: 91.9560
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  352 SER
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 57 optimal weight:    0.7980
   chunk 16 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   overall best weight:    5.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 307 GLN
C 307 GLN
D 307 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.162746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.116399 restraints weight = 5462.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.38
r_work: 0.3844 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063   4944  Z= 0.545
  Angle     :  0.845  12.773   6606  Z= 0.405
  Chirality :  0.062   0.331    744
  Planarity :  0.004   0.023    846
  Dihedral  :  7.113  25.965    654
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (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
 HIS   0.006   0.001   HIS A 362 
 PHE   0.009   0.002   PHE E 346 
 TYR   0.034   0.006   TYR E 310 
 ARG   0.001   0.000   ARG E 349 

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8840 (mttt) cc_final: 0.8468 (mtpm)
REVERT: A  353 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8180 (tttp)
REVERT: A  371 ILE cc_start: 0.8680 (mt) cc_final: 0.8257 (pp)
REVERT: B  340 LYS cc_start: 0.8029 (mttt) cc_final: 0.7809 (mtpp)
REVERT: B  343 LYS cc_start: 0.8835 (mttt) cc_final: 0.8445 (mtpm)
REVERT: B  351 GLN cc_start: 0.7701 (tt0) cc_final: 0.7115 (mt0)
REVERT: B  353 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8119 (tttm)
REVERT: B  371 ILE cc_start: 0.8819 (mt) cc_final: 0.8515 (pp)
REVERT: C  343 LYS cc_start: 0.8891 (mttt) cc_final: 0.8471 (mtpp)
REVERT: C  353 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8125 (tttp)
REVERT: C  360 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8119 (mt)
REVERT: D  343 LYS cc_start: 0.8861 (mttt) cc_final: 0.8435 (mtpp)
REVERT: D  353 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8069 (tttp)
REVERT: D  371 ILE cc_start: 0.8822 (mt) cc_final: 0.8582 (pp)
REVERT: E  343 LYS cc_start: 0.8979 (mttt) cc_final: 0.8663 (mtpm)
REVERT: E  351 GLN cc_start: 0.8359 (tt0) cc_final: 0.7973 (mt0)
REVERT: E  369 LYS cc_start: 0.4831 (pmtt) cc_final: 0.4562 (pptt)
REVERT: F  343 LYS cc_start: 0.8954 (mttt) cc_final: 0.8605 (mtpm)
REVERT: F  351 GLN cc_start: 0.8298 (tt0) cc_final: 0.7876 (mt0)
REVERT: F  368 ASN cc_start: 0.7623 (m-40) cc_final: 0.6923 (m-40)
  outliers start: 27
  outliers final: 22
  residues processed: 96
  average time/residue: 0.9191
  time to fit residues: 93.0561
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  371 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
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  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.176238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.131777 restraints weight = 5209.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 2.41
r_work: 0.4079 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3962 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4944  Z= 0.159
  Angle     :  0.699  11.776   6606  Z= 0.326
  Chirality :  0.054   0.267    744
  Planarity :  0.003   0.028    846
  Dihedral  :  6.001  23.692    654
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.63 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.26), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 330 
 PHE   0.003   0.001   PHE F 346 
 TYR   0.026   0.005   TYR E 310 
 ARG   0.002   0.000   ARG F 349 

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8788 (mttt) cc_final: 0.8431 (mtpm)
REVERT: A  351 GLN cc_start: 0.7541 (tt0) cc_final: 0.7111 (mt0)
REVERT: A  353 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8075 (tttm)
REVERT: A  371 ILE cc_start: 0.8673 (mt) cc_final: 0.8333 (pp)
REVERT: B  343 LYS cc_start: 0.8757 (mttt) cc_final: 0.8387 (mtpm)
REVERT: B  349 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7893 (mtt90)
REVERT: B  353 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7967 (tttm)
REVERT: B  371 ILE cc_start: 0.8803 (mt) cc_final: 0.8511 (pp)
REVERT: C  274 LYS cc_start: 0.6013 (mtpt) cc_final: 0.4909 (pmtt)
REVERT: C  343 LYS cc_start: 0.8929 (mttt) cc_final: 0.8538 (mtpp)
REVERT: C  349 ARG cc_start: 0.8203 (mtt180) cc_final: 0.6698 (mmp-170)
REVERT: C  360 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8080 (mt)
REVERT: D  343 LYS cc_start: 0.8912 (mttt) cc_final: 0.8502 (mtpp)
REVERT: D  349 ARG cc_start: 0.8200 (mtt180) cc_final: 0.6731 (mmp-170)
REVERT: D  353 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8147 (tttp)
REVERT: E  343 LYS cc_start: 0.8831 (mttt) cc_final: 0.8480 (mtpm)
REVERT: E  351 GLN cc_start: 0.8160 (tt0) cc_final: 0.7883 (mt0)
REVERT: E  369 LYS cc_start: 0.4762 (pmtt) cc_final: 0.4505 (pptt)
REVERT: F  343 LYS cc_start: 0.8831 (mttt) cc_final: 0.8458 (mtpm)
REVERT: F  351 GLN cc_start: 0.8076 (tt0) cc_final: 0.7730 (mt0)
REVERT: F  368 ASN cc_start: 0.8185 (m-40) cc_final: 0.7580 (m-40)
  outliers start: 21
  outliers final: 18
  residues processed: 104
  average time/residue: 1.0588
  time to fit residues: 116.0001
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
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  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  352 SER
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  325 LEU
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  371 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    0.0370
   chunk 1 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0070
   chunk 27 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   overall best weight:    0.8082

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.178717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.133566 restraints weight = 5239.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.4249 rms_B_bonded: 2.49
r_work: 0.4103 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3982 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4944  Z= 0.156
  Angle     :  0.692  11.633   6606  Z= 0.323
  Chirality :  0.054   0.239    744
  Planarity :  0.003   0.041    846
  Dihedral  :  5.719  23.229    654
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 22.70 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (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
 HIS   0.002   0.001   HIS A 299 
 PHE   0.002   0.000   PHE E 346 
 TYR   0.028   0.005   TYR F 310 
 ARG   0.001   0.000   ARG E 349 

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

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 LYS cc_start: 0.8742 (mttt) cc_final: 0.8373 (mtpm)
REVERT: A  351 GLN cc_start: 0.7504 (tt0) cc_final: 0.7165 (mt0)
REVERT: A  353 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8073 (tttp)
REVERT: A  371 ILE cc_start: 0.8621 (mt) cc_final: 0.8312 (pp)
REVERT: B  343 LYS cc_start: 0.8723 (mttt) cc_final: 0.8342 (mtpm)
REVERT: B  353 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8067 (tttm)
REVERT: B  371 ILE cc_start: 0.8747 (mt) cc_final: 0.8383 (pp)
REVERT: C  274 LYS cc_start: 0.6070 (mtpt) cc_final: 0.4719 (pmtt)
REVERT: C  343 LYS cc_start: 0.8843 (mttt) cc_final: 0.8439 (mtpp)
REVERT: C  349 ARG cc_start: 0.8202 (mtt180) cc_final: 0.6677 (mmp-170)
REVERT: C  353 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8184 (tttp)
REVERT: C  360 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8126 (mt)
REVERT: D  274 LYS cc_start: 0.6703 (mtpt) cc_final: 0.5089 (pmtt)
REVERT: D  343 LYS cc_start: 0.8779 (mttt) cc_final: 0.8356 (mtpp)
REVERT: D  349 ARG cc_start: 0.8128 (mtt180) cc_final: 0.6724 (mmp-170)
REVERT: D  353 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8213 (tttp)
REVERT: E  300 VAL cc_start: 0.9356 (t) cc_final: 0.9156 (t)
REVERT: E  325 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6109 (pt)
REVERT: E  343 LYS cc_start: 0.8806 (mttt) cc_final: 0.8426 (mtpm)
REVERT: E  351 GLN cc_start: 0.8160 (tt0) cc_final: 0.7918 (mt0)
REVERT: F  274 LYS cc_start: 0.7465 (ttpp) cc_final: 0.7234 (tttm)
REVERT: F  343 LYS cc_start: 0.8814 (mttt) cc_final: 0.8412 (mtpm)
REVERT: F  351 GLN cc_start: 0.8082 (tt0) cc_final: 0.7766 (mt0)
REVERT: F  368 ASN cc_start: 0.7943 (m-40) cc_final: 0.7328 (m-40)
  outliers start: 22
  outliers final: 16
  residues processed: 102
  average time/residue: 1.4917
  time to fit residues: 160.0015
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  360 ILE
Chi-restraints excluded: chain E residue  371 ILE
Chi-restraints excluded: chain F residue  291 CYS
Chi-restraints excluded: chain F residue  360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.169561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.123076 restraints weight = 5301.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.4104 rms_B_bonded: 2.41
r_work: 0.3959 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3841 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4944  Z= 0.312
  Angle     :  0.751  11.793   6606  Z= 0.356
  Chirality :  0.057   0.318    744
  Planarity :  0.004   0.041    846
  Dihedral  :  6.244  24.235    654
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.52 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.27), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 362 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.030   0.006   TYR F 310 
 ARG   0.001   0.000   ARG E 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4822.13 seconds
wall clock time: 88 minutes 0.20 seconds (5280.20 seconds total)