Starting phenix.real_space_refine
on Wed Feb 12 13:36:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xde_38275/02_2025/8xde_38275_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xde_38275/02_2025/8xde_38275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xde_38275/02_2025/8xde_38275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xde_38275/02_2025/8xde_38275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xde_38275/02_2025/8xde_38275_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xde_38275/02_2025/8xde_38275_neut.cif"
  }
  resolution = 2.3
  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=  -0.000 sd=   0.030
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      54      5.16       5
     C    5349      2.51       5
     N    1227      2.21       5
     O    1380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8010
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2670
          Classifications: {'peptide': 345}
          Link IDs: {'PTRANS': 19, 'TRANS': 325}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 4.93, per 1000 atoms: 0.62
  Number of scatterers: 8010
  At special positions: 0
  Unit cell: (97.58, 93.48, 69.7, 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      54     16.00
     O    1380      8.00
     N    1227      7.00
     C    5349      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: 1.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      77.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 102 through 110
    Processing helix  chain 'A' and resid 113 through 128
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 134 through 149
    Processing helix  chain 'A' and resid 149 through 170
    Processing helix  chain 'A' and resid 173 through 179
    Processing helix  chain 'A' and resid 183 through 196
    Processing helix  chain 'A' and resid 203 through 205
      No H-bonds generated for 'chain 'A' and resid 203 through 205'
    Processing helix  chain 'A' and resid 206 through 229
      removed outlier: 3.915A  pdb=" N   CYS A 217 " --> pdb=" O   THR A 213 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
      removed outlier: 3.661A  pdb=" N   ILE A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 237 through 252
    Processing helix  chain 'A' and resid 278 through 292
      removed outlier: 4.031A  pdb=" N   ILE A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 293 through 295
      No H-bonds generated for 'chain 'A' and resid 293 through 295'
    Processing helix  chain 'A' and resid 298 through 313
      removed outlier: 3.618A  pdb=" N   SER A 312 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 334
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.628A  pdb=" N   THR A 343 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 358
    Processing helix  chain 'A' and resid 365 through 392
      removed outlier: 3.864A  pdb=" N   VAL A 392 " --> pdb=" O   ASN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
    Processing helix  chain 'A' and resid 423 through 427
      removed outlier: 3.505A  pdb=" N   VAL A 427 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 440
    Processing helix  chain 'B' and resid 102 through 110
    Processing helix  chain 'B' and resid 113 through 128
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 134 through 149
    Processing helix  chain 'B' and resid 149 through 170
    Processing helix  chain 'B' and resid 173 through 179
    Processing helix  chain 'B' and resid 183 through 196
    Processing helix  chain 'B' and resid 203 through 205
      No H-bonds generated for 'chain 'B' and resid 203 through 205'
    Processing helix  chain 'B' and resid 206 through 229
      removed outlier: 3.915A  pdb=" N   CYS B 217 " --> pdb=" O   THR B 213 " (cutoff:3.500A)
      Proline residue:  B 218  - end of helix
      removed outlier: 3.661A  pdb=" N   ILE B 227 " --> pdb=" O   ALA B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 232
      No H-bonds generated for 'chain 'B' and resid 230 through 232'
    Processing helix  chain 'B' and resid 237 through 252
    Processing helix  chain 'B' and resid 278 through 292
      removed outlier: 4.033A  pdb=" N   ILE B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      Proline residue:  B 287  - end of helix
    Processing helix  chain 'B' and resid 293 through 295
      No H-bonds generated for 'chain 'B' and resid 293 through 295'
    Processing helix  chain 'B' and resid 298 through 313
      removed outlier: 3.620A  pdb=" N   SER B 312 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 334
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.630A  pdb=" N   THR B 343 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 358
    Processing helix  chain 'B' and resid 365 through 392
      removed outlier: 3.865A  pdb=" N   VAL B 392 " --> pdb=" O   ASN B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 412
    Processing helix  chain 'B' and resid 423 through 427
      removed outlier: 3.505A  pdb=" N   VAL B 427 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 440
    Processing helix  chain 'C' and resid 102 through 110
    Processing helix  chain 'C' and resid 113 through 128
    Processing helix  chain 'C' and resid 129 through 131
      No H-bonds generated for 'chain 'C' and resid 129 through 131'
    Processing helix  chain 'C' and resid 134 through 149
    Processing helix  chain 'C' and resid 149 through 170
    Processing helix  chain 'C' and resid 173 through 179
    Processing helix  chain 'C' and resid 183 through 196
    Processing helix  chain 'C' and resid 203 through 205
      No H-bonds generated for 'chain 'C' and resid 203 through 205'
    Processing helix  chain 'C' and resid 206 through 229
      removed outlier: 3.913A  pdb=" N   CYS C 217 " --> pdb=" O   THR C 213 " (cutoff:3.500A)
      Proline residue:  C 218  - end of helix
      removed outlier: 3.661A  pdb=" N   ILE C 227 " --> pdb=" O   ALA C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 232
      No H-bonds generated for 'chain 'C' and resid 230 through 232'
    Processing helix  chain 'C' and resid 237 through 252
    Processing helix  chain 'C' and resid 278 through 292
      removed outlier: 4.031A  pdb=" N   ILE C 286 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      Proline residue:  C 287  - end of helix
    Processing helix  chain 'C' and resid 293 through 295
      No H-bonds generated for 'chain 'C' and resid 293 through 295'
    Processing helix  chain 'C' and resid 298 through 313
      removed outlier: 3.620A  pdb=" N   SER C 312 " --> pdb=" O   ALA C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 334
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.628A  pdb=" N   THR C 343 " --> pdb=" O   GLU C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 358
    Processing helix  chain 'C' and resid 365 through 392
      removed outlier: 3.865A  pdb=" N   VAL C 392 " --> pdb=" O   ASN C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 412
    Processing helix  chain 'C' and resid 423 through 427
      removed outlier: 3.505A  pdb=" N   VAL C 427 " --> pdb=" O   LEU C 424 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 440

    525 hydrogen bonds defined for protein.
    1566 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: 2.27

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2355
        1.34 -     1.46: 1832
        1.46 -     1.57: 3982
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 8253
  Sorted by residual:
  bond pdb=" CA  PHE A 236 "
       pdb=" CB  PHE A 236 "
    ideal  model  delta    sigma   weight residual
    1.530  1.504  0.026 1.69e-02 3.50e+03 2.37e+00
  bond pdb=" CA  PHE C 236 "
       pdb=" CB  PHE C 236 "
    ideal  model  delta    sigma   weight residual
    1.530  1.505  0.025 1.69e-02 3.50e+03 2.27e+00
  bond pdb=" CA  PHE B 236 "
       pdb=" CB  PHE B 236 "
    ideal  model  delta    sigma   weight residual
    1.530  1.505  0.025 1.69e-02 3.50e+03 2.22e+00
  bond pdb=" CA  VAL A 235 "
       pdb=" CB  VAL A 235 "
    ideal  model  delta    sigma   weight residual
    1.528  1.540 -0.012 1.34e-02 5.57e+03 8.42e-01
  bond pdb=" CA  VAL C 235 "
       pdb=" CB  VAL C 235 "
    ideal  model  delta    sigma   weight residual
    1.528  1.539 -0.011 1.34e-02 5.57e+03 7.26e-01
  ... (remaining 8248 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 10930
        1.19 -     2.39: 308
        2.39 -     3.58: 72
        3.58 -     4.78: 9
        4.78 -     5.97: 15
  Bond angle restraints: 11334
  Sorted by residual:
  angle pdb=" N   VAL A 393 "
        pdb=" CA  VAL A 393 "
        pdb=" C   VAL A 393 "
      ideal   model   delta    sigma   weight residual
     112.29  109.32    2.97 9.40e-01 1.13e+00 1.00e+01
  angle pdb=" N   VAL B 393 "
        pdb=" CA  VAL B 393 "
        pdb=" C   VAL B 393 "
      ideal   model   delta    sigma   weight residual
     112.29  109.34    2.95 9.40e-01 1.13e+00 9.83e+00
  angle pdb=" N   VAL C 393 "
        pdb=" CA  VAL C 393 "
        pdb=" C   VAL C 393 "
      ideal   model   delta    sigma   weight residual
     112.29  109.44    2.85 9.40e-01 1.13e+00 9.22e+00
  angle pdb=" C   PHE A 212 "
        pdb=" N   THR A 213 "
        pdb=" CA  THR A 213 "
      ideal   model   delta    sigma   weight residual
     121.58  116.51    5.07 1.95e+00 2.63e-01 6.75e+00
  angle pdb=" C   PHE B 212 "
        pdb=" N   THR B 213 "
        pdb=" CA  THR B 213 "
      ideal   model   delta    sigma   weight residual
     121.58  116.59    4.99 1.95e+00 2.63e-01 6.55e+00
  ... (remaining 11329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.21: 3842
       12.21 -    24.41: 581
       24.41 -    36.62: 173
       36.62 -    48.83: 66
       48.83 -    61.03: 27
  Dihedral angle restraints: 4689
    sinusoidal: 1698
      harmonic: 2991
  Sorted by residual:
  dihedral pdb=" CA  VAL A 235 "
           pdb=" C   VAL A 235 "
           pdb=" N   PHE A 236 "
           pdb=" CA  PHE A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  VAL C 235 "
           pdb=" C   VAL C 235 "
           pdb=" N   PHE C 236 "
           pdb=" CA  PHE C 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.15  -19.85     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  VAL B 235 "
           pdb=" C   VAL B 235 "
           pdb=" N   PHE B 236 "
           pdb=" CA  PHE B 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.18  -19.82     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 4686 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 714
       0.029 -    0.057: 388
       0.057 -    0.085: 172
       0.085 -    0.114: 64
       0.114 -    0.142: 18
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CA  PRO C 430 "
            pdb=" N   PRO C 430 "
            pdb=" C   PRO C 430 "
            pdb=" CB  PRO C 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.07e-01
  chirality pdb=" CA  PRO A 430 "
            pdb=" N   PRO A 430 "
            pdb=" C   PRO A 430 "
            pdb=" CB  PRO A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CA  PRO B 430 "
            pdb=" N   PRO B 430 "
            pdb=" C   PRO B 430 "
            pdb=" CB  PRO B 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 1365
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 336 "    0.027 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO C 337 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 336 "   -0.027 5.00e-02 4.00e+02   4.16e-02 2.76e+00
        pdb=" N   PRO A 337 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 336 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO B 337 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 337 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 337 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1362 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 142
        2.70 -     3.25: 8455
        3.25 -     3.80: 14183
        3.80 -     4.35: 18509
        4.35 -     4.90: 30033
  Nonbonded interactions: 71322
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 111 "
            pdb=" NZ  LYS B 112 "
     model   vdw
     2.152 3.120
  nonbonded pdb=" OD1 ASP A 111 "
            pdb=" NZ  LYS A 112 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" OD1 ASP C 111 "
            pdb=" NZ  LYS C 112 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   ASP C 101 "
            pdb=" NH2 ARG C 124 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   ASP A 101 "
            pdb=" NH2 ARG A 124 "
     model   vdw
     2.282 3.120
  ... (remaining 71317 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'
}

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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.980
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  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:11.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
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      :  0.005   0.037   8253  Z= 0.299
  Angle     :  0.534   5.974  11334  Z= 0.292
  Chirality :  0.044   0.142   1356
  Planarity :  0.005   0.042   1365
  Dihedral  : 14.678  61.033   2775
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.22 %
    Favored  : 84.78 %
  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:  1.44 (0.27), residues: 1029
  helix:  1.26 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop :  0.40 (0.40), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.016   0.002   PHE B 361 
 TYR   0.011   0.002   TYR B 348 
 ARG   0.002   0.000   ARG C 434 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7832 (mttt)
REVERT: A  382 MET cc_start: 0.8603 (ttp) cc_final: 0.8381 (ttm)
REVERT: B  175 SER cc_start: 0.8674 (t) cc_final: 0.8351 (p)
REVERT: B  230 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8149 (mttt)
REVERT: C  175 SER cc_start: 0.8658 (t) cc_final: 0.8375 (p)
REVERT: C  230 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7770 (mttt)
REVERT: C  297 ASP cc_start: 0.8564 (p0) cc_final: 0.8322 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.9330
  time to fit residues: 117.0372
Evaluate side-chains
  101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.2886 r_free = 0.2886 target = 0.080081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.064019 restraints weight = 10151.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2584 rms_B_bonded: 1.62
r_work: 0.2480 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2373 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8253  Z= 0.260
  Angle     :  0.504   5.982  11334  Z= 0.263
  Chirality :  0.043   0.142   1356
  Planarity :  0.005   0.045   1365
  Dihedral  :  4.331  16.630   1092
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.30 %
    Favored  : 83.39 %
  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:  1.79 (0.26), residues: 1029
  helix:  1.53 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop :  0.51 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A 319 
 PHE   0.015   0.001   PHE A 361 
 TYR   0.011   0.002   TYR C 348 
 ARG   0.002   0.001   ARG B 124 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7245 (mttt)
REVERT: B  175 SER cc_start: 0.7801 (t) cc_final: 0.7511 (p)
REVERT: B  187 MET cc_start: 0.7888 (tpt) cc_final: 0.7678 (tpp)
REVERT: B  230 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7572 (mttt)
REVERT: C  175 SER cc_start: 0.7642 (t) cc_final: 0.7375 (p)
REVERT: C  230 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7160 (mttt)
REVERT: C  297 ASP cc_start: 0.8448 (p0) cc_final: 0.8228 (p0)
  outliers start: 20
  outliers final: 4
  residues processed: 108
  average time/residue: 1.0575
  time to fit residues: 122.8872
Evaluate side-chains
  98 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain B residue  435 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   chunk 6 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 101 optimal weight:    0.0770
   chunk 34 optimal weight:    7.9990
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.2936 r_free = 0.2936 target = 0.083357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.067414 restraints weight = 10319.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.2677 rms_B_bonded: 1.64
r_work: 0.2574 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2470 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8253  Z= 0.154
  Angle     :  0.450   5.809  11334  Z= 0.232
  Chirality :  0.040   0.134   1356
  Planarity :  0.005   0.047   1365
  Dihedral  :  4.077  15.889   1092
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.96 %
    Favored  : 83.74 %
  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:  2.30 (0.26), residues: 1029
  helix:  1.91 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop :  0.69 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 108 
 HIS   0.001   0.000   HIS B 319 
 PHE   0.011   0.001   PHE C 361 
 TYR   0.010   0.001   TYR C 348 
 ARG   0.001   0.000   ARG B 434 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7440 (mttt)
REVERT: A  360 MET cc_start: 0.8932 (mmm) cc_final: 0.8695 (tpp)
REVERT: B  175 SER cc_start: 0.7809 (t) cc_final: 0.7526 (p)
REVERT: B  198 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7952 (tp30)
REVERT: B  230 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7655 (mttt)
REVERT: C  108 TRP cc_start: 0.8254 (t60) cc_final: 0.8042 (t60)
REVERT: C  175 SER cc_start: 0.7646 (t) cc_final: 0.7385 (p)
REVERT: C  230 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7340 (mttt)
REVERT: C  297 ASP cc_start: 0.8444 (p0) cc_final: 0.8222 (p0)
  outliers start: 20
  outliers final: 7
  residues processed: 113
  average time/residue: 0.8954
  time to fit residues: 109.8039
Evaluate side-chains
  108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.2938 r_free = 0.2938 target = 0.083527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.067645 restraints weight = 10229.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.2684 rms_B_bonded: 1.63
r_work: 0.2583 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2479 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8253  Z= 0.156
  Angle     :  0.447   5.794  11334  Z= 0.229
  Chirality :  0.040   0.134   1356
  Planarity :  0.004   0.048   1365
  Dihedral  :  3.989  15.429   1092
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.57 %
    Favored  : 82.70 %
  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:  2.50 (0.26), residues: 1029
  helix:  2.00 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  0.93 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 366 
 HIS   0.002   0.000   HIS B 319 
 PHE   0.011   0.001   PHE A 361 
 TYR   0.009   0.001   TYR B 429 
 ARG   0.001   0.000   ARG B 434 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.8476 (tp30) cc_final: 0.8235 (mm-30)
REVERT: A  230 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7486 (mttt)
REVERT: B  175 SER cc_start: 0.7845 (t) cc_final: 0.7566 (p)
REVERT: B  198 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7897 (tp30)
REVERT: B  230 LYS cc_start: 0.8401 (mtpt) cc_final: 0.7660 (mttt)
REVERT: C  108 TRP cc_start: 0.8279 (t60) cc_final: 0.8066 (t60)
REVERT: C  175 SER cc_start: 0.7685 (t) cc_final: 0.7430 (p)
REVERT: C  198 GLU cc_start: 0.8522 (tp30) cc_final: 0.8258 (mm-30)
REVERT: C  230 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7446 (mttt)
REVERT: C  297 ASP cc_start: 0.8472 (p0) cc_final: 0.8242 (p0)
  outliers start: 15
  outliers final: 7
  residues processed: 110
  average time/residue: 0.9152
  time to fit residues: 108.9105
Evaluate side-chains
  108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 69 optimal weight:    0.1980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.2919 r_free = 0.2919 target = 0.082318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.066286 restraints weight = 10140.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2664 rms_B_bonded: 1.62
r_work: 0.2562 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2458 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8253  Z= 0.189
  Angle     :  0.460   5.851  11334  Z= 0.234
  Chirality :  0.041   0.135   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  4.014  15.827   1092
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.34 %
    Favored  : 82.93 %
  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:  2.53 (0.26), residues: 1029
  helix:  2.01 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.00 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 108 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.011   0.001   PHE B 361 
 TYR   0.010   0.001   TYR B 429 
 ARG   0.001   0.000   ARG B 124 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7533 (mttt)
REVERT: B  175 SER cc_start: 0.7877 (t) cc_final: 0.7596 (p)
REVERT: B  198 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7892 (tp30)
REVERT: B  230 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7632 (mttt)
REVERT: C  175 SER cc_start: 0.7699 (t) cc_final: 0.7447 (p)
REVERT: C  198 GLU cc_start: 0.8485 (tp30) cc_final: 0.8226 (mm-30)
REVERT: C  230 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7482 (mttt)
REVERT: C  297 ASP cc_start: 0.8473 (p0) cc_final: 0.8258 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 107
  average time/residue: 0.9840
  time to fit residues: 113.7734
Evaluate side-chains
  108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0670
   chunk 56 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.4980
   chunk 85 optimal weight:    0.0970
   chunk 83 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.2716

-------------------------------------------------------------------------------
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 = 0.2911 r_free = 0.2911 target = 0.083790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.067493 restraints weight = 10174.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2665 rms_B_bonded: 1.69
r_work: 0.2553 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2447 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8253  Z= 0.134
  Angle     :  0.442   6.500  11334  Z= 0.224
  Chirality :  0.040   0.131   1356
  Planarity :  0.004   0.048   1365
  Dihedral  :  3.863  15.334   1092
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.15 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.73 (0.26), residues: 1029
  helix:  2.17 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.02 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 108 
 HIS   0.001   0.000   HIS C 319 
 PHE   0.009   0.001   PHE C 361 
 TYR   0.009   0.001   TYR B 348 
 ARG   0.001   0.000   ARG B 434 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7862 (mm)
REVERT: A  230 LYS cc_start: 0.8541 (mtpt) cc_final: 0.7733 (mttt)
REVERT: B  175 SER cc_start: 0.8114 (t) cc_final: 0.7841 (p)
REVERT: B  198 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8112 (tp30)
REVERT: B  230 LYS cc_start: 0.8479 (mtpt) cc_final: 0.7756 (mttt)
REVERT: C  175 SER cc_start: 0.7943 (t) cc_final: 0.7690 (p)
REVERT: C  198 GLU cc_start: 0.8641 (tp30) cc_final: 0.8412 (mm-30)
REVERT: C  230 LYS cc_start: 0.8470 (mtpt) cc_final: 0.7682 (mttt)
REVERT: C  297 ASP cc_start: 0.8601 (p0) cc_final: 0.8387 (p0)
  outliers start: 14
  outliers final: 7
  residues processed: 109
  average time/residue: 0.9233
  time to fit residues: 109.2239
Evaluate side-chains
  109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 34 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.2873 r_free = 0.2873 target = 0.080546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.064207 restraints weight = 10186.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2587 rms_B_bonded: 1.66
r_work: 0.2480 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2372 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8253  Z= 0.240
  Angle     :  0.491   7.510  11334  Z= 0.249
  Chirality :  0.042   0.136   1356
  Planarity :  0.004   0.050   1365
  Dihedral  :  4.073  14.755   1092
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.61 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.26), residues: 1029
  helix:  2.03 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.06 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 319 
 PHE   0.012   0.001   PHE B 361 
 TYR   0.012   0.001   TYR B 429 
 ARG   0.002   0.000   ARG C 124 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7514 (mttt)
REVERT: B  175 SER cc_start: 0.7961 (t) cc_final: 0.7678 (p)
REVERT: B  198 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7948 (tp30)
REVERT: B  230 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7608 (mttt)
REVERT: C  175 SER cc_start: 0.7741 (t) cc_final: 0.7499 (p)
REVERT: C  198 GLU cc_start: 0.8524 (tp30) cc_final: 0.8285 (mm-30)
REVERT: C  230 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7475 (mttt)
REVERT: C  297 ASP cc_start: 0.8530 (p0) cc_final: 0.8312 (p0)
  outliers start: 13
  outliers final: 7
  residues processed: 103
  average time/residue: 1.0103
  time to fit residues: 112.1050
Evaluate side-chains
  103 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.2882 r_free = 0.2882 target = 0.081008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.064690 restraints weight = 10269.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2594 rms_B_bonded: 1.66
r_work: 0.2486 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2379 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8253  Z= 0.220
  Angle     :  0.477   6.546  11334  Z= 0.244
  Chirality :  0.042   0.138   1356
  Planarity :  0.004   0.050   1365
  Dihedral  :  4.063  14.715   1092
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.49 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.26), residues: 1029
  helix:  2.04 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.05 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 319 
 PHE   0.015   0.001   PHE B 361 
 TYR   0.012   0.001   TYR B 429 
 ARG   0.001   0.000   ARG C 124 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7482 (mttt)
REVERT: B  175 SER cc_start: 0.7911 (t) cc_final: 0.7634 (p)
REVERT: B  198 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7908 (tp30)
REVERT: B  230 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7567 (mttt)
REVERT: C  175 SER cc_start: 0.7662 (t) cc_final: 0.7418 (p)
REVERT: C  198 GLU cc_start: 0.8491 (tp30) cc_final: 0.8264 (mm-30)
REVERT: C  230 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7451 (mttt)
REVERT: C  297 ASP cc_start: 0.8489 (p0) cc_final: 0.8283 (p0)
  outliers start: 14
  outliers final: 8
  residues processed: 100
  average time/residue: 0.9593
  time to fit residues: 103.4316
Evaluate side-chains
  102 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.2897 r_free = 0.2897 target = 0.081938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.065652 restraints weight = 10276.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2612 rms_B_bonded: 1.67
r_work: 0.2504 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2396 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8253  Z= 0.181
  Angle     :  0.478   8.634  11334  Z= 0.241
  Chirality :  0.041   0.146   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  4.013  15.105   1092
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 16.49 %
    Favored  : 82.12 %
  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:  2.66 (0.26), residues: 1029
  helix:  2.10 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.05 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.002   0.000   HIS B 319 
 PHE   0.012   0.001   PHE B 361 
 TYR   0.010   0.001   TYR C 247 
 ARG   0.001   0.000   ARG B 124 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7492 (mttt)
REVERT: B  175 SER cc_start: 0.7894 (t) cc_final: 0.7624 (p)
REVERT: B  198 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7890 (tp30)
REVERT: B  230 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7516 (mttt)
REVERT: C  175 SER cc_start: 0.7636 (t) cc_final: 0.7400 (p)
REVERT: C  198 GLU cc_start: 0.8475 (tp30) cc_final: 0.8252 (mm-30)
REVERT: C  230 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7658 (mttt)
REVERT: C  297 ASP cc_start: 0.8481 (p0) cc_final: 0.8271 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 102
  average time/residue: 0.9674
  time to fit residues: 106.6849
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  354 CYS
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0170
   chunk 98 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    0.6018

-------------------------------------------------------------------------------
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 = 0.2908 r_free = 0.2908 target = 0.082738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.066689 restraints weight = 10214.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.2630 rms_B_bonded: 1.65
r_work: 0.2523 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2415 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8253  Z= 0.169
  Angle     :  0.471   9.025  11334  Z= 0.237
  Chirality :  0.041   0.140   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  3.958  15.367   1092
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 17.07 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.26), residues: 1029
  helix:  2.15 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.05 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 366 
 HIS   0.002   0.000   HIS B 319 
 PHE   0.011   0.001   PHE B 361 
 TYR   0.010   0.001   TYR C 247 
 ARG   0.001   0.000   ARG B 124 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7533 (mttt)
REVERT: B  175 SER cc_start: 0.7959 (t) cc_final: 0.7681 (p)
REVERT: B  198 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7911 (tp30)
REVERT: B  230 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7552 (mttt)
REVERT: C  175 SER cc_start: 0.7694 (t) cc_final: 0.7451 (p)
REVERT: C  198 GLU cc_start: 0.8515 (tp30) cc_final: 0.8301 (mm-30)
REVERT: C  230 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7684 (mttt)
  outliers start: 9
  outliers final: 8
  residues processed: 99
  average time/residue: 1.0298
  time to fit residues: 109.9494
Evaluate side-chains
  105 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  273 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.2896 r_free = 0.2896 target = 0.081935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.065651 restraints weight = 10278.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.2613 rms_B_bonded: 1.67
r_work: 0.2506 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2398 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8253  Z= 0.194
  Angle     :  0.485   9.115  11334  Z= 0.245
  Chirality :  0.041   0.143   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  3.990  15.216   1092
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.72 %
    Favored  : 82.01 %
  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:  2.69 (0.26), residues: 1029
  helix:  2.13 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.06 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.013   0.001   PHE B 361 
 TYR   0.010   0.001   TYR B 429 
 ARG   0.001   0.000   ARG B 124 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5088.00 seconds
wall clock time: 90 minutes 41.42 seconds (5441.42 seconds total)