Starting phenix.real_space_refine
on Fri Aug 22 21:11:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xde_38275/08_2025/8xde_38275_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xde_38275/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xde_38275/08_2025/8xde_38275_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xde_38275/08_2025/8xde_38275_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xde_38275/08_2025/8xde_38275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xde_38275/08_2025/8xde_38275.map"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C
  Time building chain proxies: 1.99, per 1000 atoms: 0.25
  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: 0.72
  Conformation dependent library (CDL) restraints added in 425.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.25
  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: 1.32

  Time building geometry restraints manager: 0.93 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.630
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.220
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.900
-------------------------------------------------------------------------------
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= 0.200
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.27), 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
 ARG   0.002   0.000   ARG C 434 
 TYR   0.011   0.002   TYR B 348 
 PHE   0.016   0.002   PHE B 361 
 TRP   0.017   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 8253)
  covalent geometry    : angle       0.53417 (11334)
  hydrogen bonds       : bond        0.11028 (  525)
  hydrogen bonds       : angle       5.45894 ( 1566)

*********************** 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  : 0.314 
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: 0.4545
  time to fit residues: 56.9938
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  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.2892 r_free = 0.2892 target = 0.080442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.064445 restraints weight = 10293.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.2591 rms_B_bonded: 1.62
r_work: 0.2486 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2380 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.0935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8253  Z= 0.161
  Angle     :  0.496   5.953  11334  Z= 0.259
  Chirality :  0.042   0.141   1356
  Planarity :  0.005   0.045   1365
  Dihedral  :  4.309  16.379   1092
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.42 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.26), residues: 1029
  helix:  1.54 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop :  0.53 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 174 
 TYR   0.011   0.002   TYR C 348 
 PHE   0.014   0.001   PHE C 361 
 TRP   0.014   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8253)
  covalent geometry    : angle       0.49569 (11334)
  hydrogen bonds       : bond        0.04509 (  525)
  hydrogen bonds       : angle       4.03005 ( 1566)

*********************** 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: 19
    poor density    : 97
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7254 (mttt)
REVERT: B  175 SER cc_start: 0.7790 (t) cc_final: 0.7497 (p)
REVERT: B  230 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7615 (mttt)
REVERT: C  175 SER cc_start: 0.7638 (t) cc_final: 0.7376 (p)
REVERT: C  230 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7172 (mttt)
REVERT: C  277 MET cc_start: 0.7079 (ttp) cc_final: 0.6824 (tpp)
REVERT: C  297 ASP cc_start: 0.8443 (p0) cc_final: 0.8226 (p0)
  outliers start: 19
  outliers final: 4
  residues processed: 109
  average time/residue: 0.5008
  time to fit residues: 58.5685
Evaluate side-chains
  99 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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 95 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 50 optimal weight:    0.3980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.2907 r_free = 0.2907 target = 0.081636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.065764 restraints weight = 10173.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2646 rms_B_bonded: 1.61
r_work: 0.2543 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2439 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1146

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= 0.128
  Angle     :  0.464   5.869  11334  Z= 0.239
  Chirality :  0.041   0.136   1356
  Planarity :  0.005   0.048   1365
  Dihedral  :  4.168  15.696   1092
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.61 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.26), residues: 1029
  helix:  1.83 (0.19), residues: 741
  sheet:  None (None), residues: 0
  loop :  0.78 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 434 
 TYR   0.010   0.001   TYR B 429 
 PHE   0.012   0.001   PHE C 361 
 TRP   0.010   0.001   TRP C 366 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8253)
  covalent geometry    : angle       0.46438 (11334)
  hydrogen bonds       : bond        0.04089 (  525)
  hydrogen bonds       : angle       3.78238 ( 1566)

*********************** 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
  116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7451 (mttt)
REVERT: B  175 SER cc_start: 0.7835 (t) cc_final: 0.7539 (p)
REVERT: B  198 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7851 (tp30)
REVERT: B  230 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7717 (mttt)
REVERT: B  370 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6915 (mp)
REVERT: C  175 SER cc_start: 0.7669 (t) cc_final: 0.7406 (p)
REVERT: C  230 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7342 (mttt)
REVERT: C  297 ASP cc_start: 0.8458 (p0) cc_final: 0.8235 (p0)
  outliers start: 20
  outliers final: 7
  residues processed: 108
  average time/residue: 0.4399
  time to fit residues: 51.4186
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  : 0.313 
-------------------------------------------------------------------------------
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 B residue  370 LEU
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 28 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.079995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.063870 restraints weight = 10404.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2579 rms_B_bonded: 1.64
r_work: 0.2475 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2369 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1239

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= 0.164
  Angle     :  0.487   5.977  11334  Z= 0.250
  Chirality :  0.042   0.141   1356
  Planarity :  0.005   0.049   1365
  Dihedral  :  4.223  15.425   1092
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.61 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.26), residues: 1029
  helix:  1.80 (0.19), residues: 741
  sheet:  None (None), residues: 0
  loop :  0.95 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 124 
 TYR   0.011   0.001   TYR B 429 
 PHE   0.013   0.001   PHE C 361 
 TRP   0.009   0.001   TRP C 366 
 HIS   0.003   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8253)
  covalent geometry    : angle       0.48663 (11334)
  hydrogen bonds       : bond        0.04309 (  525)
  hydrogen bonds       : angle       3.80955 ( 1566)

*********************** 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
  115 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7397 (mttt)
REVERT: B  175 SER cc_start: 0.7835 (t) cc_final: 0.7537 (p)
REVERT: B  198 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7846 (tp30)
REVERT: B  230 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7588 (mttt)
REVERT: B  370 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6921 (mp)
REVERT: C  175 SER cc_start: 0.7649 (t) cc_final: 0.7396 (p)
REVERT: C  230 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7377 (mttt)
REVERT: C  297 ASP cc_start: 0.8472 (p0) cc_final: 0.8241 (p0)
  outliers start: 21
  outliers final: 10
  residues processed: 104
  average time/residue: 0.4604
  time to fit residues: 51.7929
Evaluate side-chains
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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  112 LYS
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 B residue  370 LEU
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 37 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.2909 r_free = 0.2909 target = 0.081922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.065914 restraints weight = 10324.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.2617 rms_B_bonded: 1.64
r_work: 0.2513 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2408 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8253  Z= 0.118
  Angle     :  0.459   5.851  11334  Z= 0.235
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  4.097  15.482   1092
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.26), residues: 1029
  helix:  1.97 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  0.98 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 434 
 TYR   0.010   0.001   TYR B 429 
 PHE   0.011   0.001   PHE C 361 
 TRP   0.011   0.001   TRP C 366 
 HIS   0.002   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8253)
  covalent geometry    : angle       0.45866 (11334)
  hydrogen bonds       : bond        0.03912 (  525)
  hydrogen bonds       : angle       3.67579 ( 1566)

*********************** 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
  115 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.8440 (tp30) cc_final: 0.8226 (mm-30)
REVERT: A  230 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7499 (mttt)
REVERT: B  175 SER cc_start: 0.7830 (t) cc_final: 0.7546 (p)
REVERT: B  198 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7837 (tp30)
REVERT: B  230 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7527 (mttt)
REVERT: C  175 SER cc_start: 0.7634 (t) cc_final: 0.7389 (p)
REVERT: C  198 GLU cc_start: 0.8464 (tp30) cc_final: 0.8167 (mm-30)
REVERT: C  230 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7422 (mttt)
REVERT: C  297 ASP cc_start: 0.8469 (p0) cc_final: 0.8234 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 0.4437
  time to fit residues: 51.8750
Evaluate side-chains
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  112 LYS
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 C residue  114 LEU
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 13 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.2903 r_free = 0.2903 target = 0.080246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.064438 restraints weight = 10326.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.2661 rms_B_bonded: 1.64
r_work: 0.2562 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2459 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8253  Z= 0.177
  Angle     :  0.499   6.191  11334  Z= 0.255
  Chirality :  0.043   0.141   1356
  Planarity :  0.005   0.050   1365
  Dihedral  :  4.219  15.196   1092
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.26), residues: 1029
  helix:  1.88 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.02 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 124 
 TYR   0.011   0.001   TYR B 429 
 PHE   0.013   0.001   PHE B 361 
 TRP   0.013   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8253)
  covalent geometry    : angle       0.49861 (11334)
  hydrogen bonds       : bond        0.04350 (  525)
  hydrogen bonds       : angle       3.79596 ( 1566)

*********************** 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
  106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.8456 (tp30) cc_final: 0.8248 (mm-30)
REVERT: A  230 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7486 (mttt)
REVERT: B  175 SER cc_start: 0.7908 (t) cc_final: 0.7604 (p)
REVERT: B  198 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7878 (tp30)
REVERT: B  230 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7570 (mttt)
REVERT: B  370 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6957 (mp)
REVERT: C  175 SER cc_start: 0.7702 (t) cc_final: 0.7445 (p)
REVERT: C  198 GLU cc_start: 0.8454 (tp30) cc_final: 0.8193 (mm-30)
REVERT: C  230 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7477 (mttt)
REVERT: C  297 ASP cc_start: 0.8507 (p0) cc_final: 0.8263 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 99
  average time/residue: 0.4883
  time to fit residues: 52.0305
Evaluate side-chains
  104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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 B residue  354 CYS
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain C residue  114 LEU
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 80 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.080665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.064605 restraints weight = 10226.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2592 rms_B_bonded: 1.64
r_work: 0.2484 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2376 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8253  Z= 0.132
  Angle     :  0.476   6.966  11334  Z= 0.243
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  4.130  15.107   1092
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.92 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.26), residues: 1029
  helix:  1.97 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.03 (0.40), residues: 288

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8253)
  covalent geometry    : angle       0.47647 (11334)
  hydrogen bonds       : bond        0.04040 (  525)
  hydrogen bonds       : angle       3.70501 ( 1566)

*********************** 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
  107 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.8455 (tp30) cc_final: 0.8242 (mm-30)
REVERT: A  230 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7496 (mttt)
REVERT: B  175 SER cc_start: 0.7897 (t) cc_final: 0.7617 (p)
REVERT: B  198 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7886 (tp30)
REVERT: B  230 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7498 (mttt)
REVERT: C  175 SER cc_start: 0.7658 (t) cc_final: 0.7417 (p)
REVERT: C  198 GLU cc_start: 0.8451 (tp30) cc_final: 0.8203 (mm-30)
REVERT: C  230 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7462 (mttt)
REVERT: C  297 ASP cc_start: 0.8485 (p0) cc_final: 0.8275 (p0)
  outliers start: 14
  outliers final: 9
  residues processed: 101
  average time/residue: 0.4508
  time to fit residues: 49.2232
Evaluate side-chains
  103 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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 A residue  370 LEU
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  387 SER
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 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0570
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6698

-------------------------------------------------------------------------------
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 = 0.2890 r_free = 0.2890 target = 0.081713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.065653 restraints weight = 10222.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2610 rms_B_bonded: 1.65
r_work: 0.2503 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2395 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8253  Z= 0.121
  Angle     :  0.471   7.294  11334  Z= 0.239
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  4.048  14.995   1092
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.57 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.26), residues: 1029
  helix:  2.05 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.08 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 124 
 TYR   0.010   0.001   TYR B 348 
 PHE   0.011   0.001   PHE B 361 
 TRP   0.011   0.001   TRP C 366 
 HIS   0.002   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8253)
  covalent geometry    : angle       0.47060 (11334)
  hydrogen bonds       : bond        0.03892 (  525)
  hydrogen bonds       : angle       3.63976 ( 1566)

*********************** 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
  109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.8441 (tp30) cc_final: 0.8227 (mm-30)
REVERT: A  230 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7540 (mttt)
REVERT: B  175 SER cc_start: 0.7901 (t) cc_final: 0.7623 (p)
REVERT: B  198 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7904 (tp30)
REVERT: B  230 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7523 (mttt)
REVERT: B  370 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6965 (mp)
REVERT: C  175 SER cc_start: 0.7655 (t) cc_final: 0.7419 (p)
REVERT: C  198 GLU cc_start: 0.8440 (tp30) cc_final: 0.8185 (mm-30)
REVERT: C  230 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7618 (mttt)
REVERT: C  297 ASP cc_start: 0.8483 (p0) cc_final: 0.8268 (p0)
  outliers start: 16
  outliers final: 9
  residues processed: 103
  average time/residue: 0.4269
  time to fit residues: 47.5345
Evaluate side-chains
  104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
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 A residue  370 LEU
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  370 LEU
Chi-restraints excluded: chain B residue  387 SER
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 31 optimal weight:    0.0050
   chunk 85 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 18 optimal weight:    0.3980
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 = 0.2934 r_free = 0.2934 target = 0.084384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.068484 restraints weight = 10221.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.2660 rms_B_bonded: 1.65
r_work: 0.2554 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2447 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8253  Z= 0.104
  Angle     :  0.459   8.773  11334  Z= 0.231
  Chirality :  0.040   0.135   1356
  Planarity :  0.004   0.048   1365
  Dihedral  :  3.881  15.322   1092
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.26), residues: 1029
  helix:  2.20 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.05 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 434 
 TYR   0.010   0.001   TYR B 348 
 PHE   0.009   0.001   PHE B 361 
 TRP   0.012   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8253)
  covalent geometry    : angle       0.45873 (11334)
  hydrogen bonds       : bond        0.03595 (  525)
  hydrogen bonds       : angle       3.50502 ( 1566)

*********************** 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
  116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7539 (mttt)
REVERT: B  175 SER cc_start: 0.7859 (t) cc_final: 0.7593 (p)
REVERT: B  198 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7859 (tp30)
REVERT: B  230 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7504 (mttt)
REVERT: C  175 SER cc_start: 0.7688 (t) cc_final: 0.7457 (p)
REVERT: C  198 GLU cc_start: 0.8438 (tp30) cc_final: 0.8190 (mm-30)
REVERT: C  230 LYS cc_start: 0.8373 (mtpt) cc_final: 0.7695 (mttt)
REVERT: C  399 THR cc_start: 0.7454 (p) cc_final: 0.7210 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 111
  average time/residue: 0.4226
  time to fit residues: 50.9248
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  : 0.308 
-------------------------------------------------------------------------------
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 A residue  370 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  387 SER
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 66 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.2899 r_free = 0.2899 target = 0.082075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.065902 restraints weight = 10273.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2615 rms_B_bonded: 1.66
r_work: 0.2508 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2399 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8253  Z= 0.132
  Angle     :  0.490   9.062  11334  Z= 0.249
  Chirality :  0.041   0.144   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  3.986  14.478   1092
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.72 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.26), residues: 1029
  helix:  2.16 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.11 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.010   0.001   TYR B 429 
 PHE   0.013   0.001   PHE B 361 
 TRP   0.014   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8253)
  covalent geometry    : angle       0.48987 (11334)
  hydrogen bonds       : bond        0.03843 (  525)
  hydrogen bonds       : angle       3.57438 ( 1566)

********************** 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
  110 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7558 (mttt)
REVERT: B  175 SER cc_start: 0.7963 (t) cc_final: 0.7682 (p)
REVERT: B  198 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7939 (tp30)
REVERT: B  230 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7547 (mttt)
REVERT: C  175 SER cc_start: 0.7710 (t) cc_final: 0.7468 (p)
REVERT: C  198 GLU cc_start: 0.8491 (tp30) cc_final: 0.8261 (mm-30)
REVERT: C  230 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7697 (mttt)
  outliers start: 15
  outliers final: 9
  residues processed: 104
  average time/residue: 0.4271
  time to fit residues: 48.0346
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  : 0.297 
-------------------------------------------------------------------------------
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 A residue  370 LEU
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 B residue  387 SER
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 71 optimal weight:    0.2980
   chunk 87 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.2906 r_free = 0.2906 target = 0.082602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.066491 restraints weight = 10144.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.2626 rms_B_bonded: 1.65
r_work: 0.2520 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2412 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8253  Z= 0.119
  Angle     :  0.477   8.752  11334  Z= 0.242
  Chirality :  0.041   0.138   1356
  Planarity :  0.004   0.049   1365
  Dihedral  :  3.971  14.515   1092
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.72 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.26), residues: 1029
  helix:  2.20 (0.18), residues: 741
  sheet:  None (None), residues: 0
  loop :  1.10 (0.40), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.009   0.001   TYR C 348 
 PHE   0.013   0.001   PHE B 361 
 TRP   0.014   0.001   TRP B 108 
 HIS   0.002   0.000   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8253)
  covalent geometry    : angle       0.47729 (11334)
  hydrogen bonds       : bond        0.03717 (  525)
  hydrogen bonds       : angle       3.53605 ( 1566)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2779.62 seconds
wall clock time: 48 minutes 18.57 seconds (2898.57 seconds total)