Starting phenix.real_space_refine
on Thu Mar 13 11:25:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8trm_41583/03_2025/8trm_41583.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8trm_41583/03_2025/8trm_41583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8trm_41583/03_2025/8trm_41583.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8trm_41583/03_2025/8trm_41583.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8trm_41583/03_2025/8trm_41583.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8trm_41583/03_2025/8trm_41583.cif"
  }
  resolution = 2.5
  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=   0.359
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      3      5.21       5
     S      57      5.16       5
     C    5544      2.51       5
     N    1470      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8814
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "C"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.91, per 1000 atoms: 0.78
  Number of scatterers: 8814
  At special positions: 0
  Unit cell: (77.464, 99.356, 138.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      57     16.00
     P       6     15.00
     Mg      3     11.99
     O    1734      8.00
     N    1470      7.00
     C    5544      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: 2.26
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 18 sheets defined
      50.1% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 79 through 93
    Processing helix  chain 'A' and resid 113 through 127
      removed outlier: 4.018A  pdb=" N   ARG A 117 " --> pdb=" O   PRO A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 146
    Processing helix  chain 'A' and resid 173 through 176
    Processing helix  chain 'A' and resid 182 through 194
    Processing helix  chain 'A' and resid 195 through 198
    Processing helix  chain 'A' and resid 203 through 218
    Processing helix  chain 'A' and resid 223 through 232
    Processing helix  chain 'A' and resid 253 through 258
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 274 through 285
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.575A  pdb=" N   THR A 305 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 322
    Processing helix  chain 'A' and resid 335 through 337
      No H-bonds generated for 'chain 'A' and resid 335 through 337'
    Processing helix  chain 'A' and resid 338 through 349
    Processing helix  chain 'A' and resid 350 through 356
      removed outlier: 3.540A  pdb=" N   GLN A 354 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLN A 355 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 367
    Processing helix  chain 'A' and resid 369 through 375
      removed outlier: 4.113A  pdb=" N   ARG A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 62
    Processing helix  chain 'B' and resid 79 through 93
    Processing helix  chain 'B' and resid 113 through 127
      removed outlier: 4.019A  pdb=" N   ARG B 117 " --> pdb=" O   PRO B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 146
    Processing helix  chain 'B' and resid 173 through 176
    Processing helix  chain 'B' and resid 182 through 194
    Processing helix  chain 'B' and resid 195 through 198
    Processing helix  chain 'B' and resid 203 through 218
    Processing helix  chain 'B' and resid 223 through 232
    Processing helix  chain 'B' and resid 253 through 258
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 264 through 269
    Processing helix  chain 'B' and resid 274 through 285
    Processing helix  chain 'B' and resid 290 through 297
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.575A  pdb=" N   THR B 305 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 322
    Processing helix  chain 'B' and resid 335 through 337
      No H-bonds generated for 'chain 'B' and resid 335 through 337'
    Processing helix  chain 'B' and resid 338 through 349
    Processing helix  chain 'B' and resid 350 through 356
      removed outlier: 3.540A  pdb=" N   GLN B 354 " --> pdb=" O   SER B 351 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN B 355 " --> pdb=" O   THR B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 367
    Processing helix  chain 'B' and resid 369 through 375
      removed outlier: 4.113A  pdb=" N   ARG B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 62
    Processing helix  chain 'C' and resid 79 through 93
    Processing helix  chain 'C' and resid 113 through 127
      removed outlier: 4.018A  pdb=" N   ARG C 117 " --> pdb=" O   PRO C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 146
    Processing helix  chain 'C' and resid 173 through 176
    Processing helix  chain 'C' and resid 182 through 194
    Processing helix  chain 'C' and resid 195 through 198
    Processing helix  chain 'C' and resid 203 through 218
    Processing helix  chain 'C' and resid 223 through 232
    Processing helix  chain 'C' and resid 253 through 258
    Processing helix  chain 'C' and resid 259 through 263
    Processing helix  chain 'C' and resid 264 through 269
    Processing helix  chain 'C' and resid 274 through 285
    Processing helix  chain 'C' and resid 290 through 297
    Processing helix  chain 'C' and resid 302 through 306
      removed outlier: 3.574A  pdb=" N   THR C 305 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 309 through 322
    Processing helix  chain 'C' and resid 335 through 337
      No H-bonds generated for 'chain 'C' and resid 335 through 337'
    Processing helix  chain 'C' and resid 338 through 349
    Processing helix  chain 'C' and resid 350 through 356
      removed outlier: 3.540A  pdb=" N   GLN C 354 " --> pdb=" O   SER C 351 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLN C 355 " --> pdb=" O   THR C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 367
    Processing helix  chain 'C' and resid 369 through 375
      removed outlier: 4.113A  pdb=" N   ARG C 373 " --> pdb=" O   SER C 369 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33
      removed outlier: 6.669A  pdb=" N   LEU A   9 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR A 107 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 8.368A  pdb=" N   VAL A  11 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 171
      removed outlier: 6.832A  pdb=" N   VAL A 298 " --> pdb=" O   VAL A 331 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242
    Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33
      removed outlier: 6.669A  pdb=" N   LEU B   9 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR B 107 " --> pdb=" O   LEU B   9 " (cutoff:3.500A)
      removed outlier: 8.368A  pdb=" N   VAL B  11 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55
    Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73
    Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171
    Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171
      removed outlier: 6.832A  pdb=" N   VAL B 298 " --> pdb=" O   VAL B 331 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242
    Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 33
      removed outlier: 6.669A  pdb=" N   LEU C   9 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   THR C 107 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   VAL C  11 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55
    Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 73
    Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 171
    Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171
      removed outlier: 6.832A  pdb=" N   VAL C 298 " --> pdb=" O   VAL C 331 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 242

    447 hydrogen bonds defined for protein.
    1143 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: 2.72

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2870
        1.34 -     1.46: 1656
        1.46 -     1.57: 4339
        1.57 -     1.69: 9
        1.69 -     1.81: 99
  Bond restraints: 8973
  Sorted by residual:
  bond pdb=" N   ASP B 212 "
       pdb=" CA  ASP B 212 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.19e-02 7.06e+03 4.76e+00
  bond pdb=" N   ASP C 212 "
       pdb=" CA  ASP C 212 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.025 1.19e-02 7.06e+03 4.55e+00
  bond pdb=" N   ASP A 212 "
       pdb=" CA  ASP A 212 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.025 1.19e-02 7.06e+03 4.50e+00
  bond pdb=" C4  ADP C 402 "
       pdb=" C5  ADP C 402 "
    ideal  model  delta    sigma   weight residual
    1.490  1.466  0.024 2.00e-02 2.50e+03 1.43e+00
  bond pdb=" C4  ADP A 402 "
       pdb=" C5  ADP A 402 "
    ideal  model  delta    sigma   weight residual
    1.490  1.466  0.024 2.00e-02 2.50e+03 1.43e+00
  ... (remaining 8968 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 11802
        1.41 -     2.82: 247
        2.82 -     4.24: 86
        4.24 -     5.65: 13
        5.65 -     7.06: 14
  Bond angle restraints: 12162
  Sorted by residual:
  angle pdb=" N   ILE C 290 "
        pdb=" CA  ILE C 290 "
        pdb=" C   ILE C 290 "
      ideal   model   delta    sigma   weight residual
     113.42  109.06    4.36 1.17e+00 7.31e-01 1.39e+01
  angle pdb=" N   ILE B 290 "
        pdb=" CA  ILE B 290 "
        pdb=" C   ILE B 290 "
      ideal   model   delta    sigma   weight residual
     113.42  109.06    4.36 1.17e+00 7.31e-01 1.39e+01
  angle pdb=" N   ILE A 290 "
        pdb=" CA  ILE A 290 "
        pdb=" C   ILE A 290 "
      ideal   model   delta    sigma   weight residual
     113.42  109.07    4.35 1.17e+00 7.31e-01 1.38e+01
  angle pdb=" CA  ILE A 290 "
        pdb=" C   ILE A 290 "
        pdb=" N   ARG A 291 "
      ideal   model   delta    sigma   weight residual
     118.90  115.55    3.35 9.40e-01 1.13e+00 1.27e+01
  angle pdb=" CA  ILE B 290 "
        pdb=" C   ILE B 290 "
        pdb=" N   ARG B 291 "
      ideal   model   delta    sigma   weight residual
     118.90  115.58    3.32 9.40e-01 1.13e+00 1.25e+01
  ... (remaining 12157 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.62: 5010
       28.62 -    57.24: 351
       57.24 -    85.86: 36
       85.86 -   114.48: 3
      114.48 -   143.10: 6
  Dihedral angle restraints: 5406
    sinusoidal: 2205
      harmonic: 3201
  Sorted by residual:
  dihedral pdb=" O1B ADP C 402 "
           pdb=" O3A ADP C 402 "
           pdb=" PB  ADP C 402 "
           pdb=" PA  ADP C 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   83.10 -143.10     1      2.00e+01 2.50e-03 4.32e+01
  dihedral pdb=" O1B ADP B 402 "
           pdb=" O3A ADP B 402 "
           pdb=" PB  ADP B 402 "
           pdb=" PA  ADP B 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   83.07 -143.08     1      2.00e+01 2.50e-03 4.32e+01
  dihedral pdb=" O1B ADP A 402 "
           pdb=" O3A ADP A 402 "
           pdb=" PB  ADP A 402 "
           pdb=" PA  ADP A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   83.05 -143.05     1      2.00e+01 2.50e-03 4.32e+01
  ... (remaining 5403 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 654
       0.027 -    0.053: 378
       0.053 -    0.080: 156
       0.080 -    0.106: 122
       0.106 -    0.133: 34
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ILE B 358 "
            pdb=" N   ILE B 358 "
            pdb=" C   ILE B 358 "
            pdb=" CB  ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE C 358 "
            pdb=" N   ILE C 358 "
            pdb=" C   ILE C 358 "
            pdb=" CB  ILE C 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 1341 not shown)

  Planarity restraints: 1557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 164 "    0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO A 165 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 165 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 165 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 164 "   -0.020 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO B 165 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 165 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 165 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 164 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO C 165 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 165 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 165 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1554 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 42
        2.51 -     3.11: 5956
        3.11 -     3.70: 13252
        3.70 -     4.30: 20131
        4.30 -     4.90: 32954
  Nonbonded interactions: 72335
  Sorted by model distance:
  nonbonded pdb="MG    MG A 401 "
            pdb=" O   HOH A 507 "
     model   vdw
     1.909 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O   HOH B 507 "
     model   vdw
     1.909 2.170
  nonbonded pdb="MG    MG C 401 "
            pdb=" O   HOH C 507 "
     model   vdw
     1.909 2.170
  nonbonded pdb="MG    MG A 401 "
            pdb=" O   HOH A 503 "
     model   vdw
     1.921 2.170
  nonbonded pdb="MG    MG C 401 "
            pdb=" O   HOH C 503 "
     model   vdw
     1.921 2.170
  ... (remaining 72330 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:             34.800
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.910
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  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:10.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   71.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
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      :  0.003   0.029   8973  Z= 0.205
  Angle     :  0.606   7.058  12162  Z= 0.310
  Chirality :  0.047   0.133   1344
  Planarity :  0.004   0.031   1557
  Dihedral  : 18.288 143.104   3360
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.67 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.26), residues: 1107
  helix:  0.82 (0.25), residues: 459
  sheet:  0.95 (0.37), residues: 186
  loop :  1.55 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  80 
 HIS   0.003   0.001   HIS A 102 
 PHE   0.007   0.001   PHE C 256 
 TYR   0.009   0.001   TYR A 295 
 ARG   0.001   0.000   ARG A 257 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 201
  time to evaluate  : 1.408 
Fit side-chains
REVERT: A  177 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8825 (mtm)
REVERT: B   96 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7906 (mtm-85)
REVERT: B  168 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8460 (mm-30)
REVERT: B  180 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7709 (t0)
REVERT: B  226 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7429 (mt-10)
REVERT: B  229 LYS cc_start: 0.7756 (mtpm) cc_final: 0.7488 (mttm)
REVERT: B  287 ASP cc_start: 0.8178 (m-30) cc_final: 0.7974 (m-30)
REVERT: B  293 ASP cc_start: 0.8327 (m-30) cc_final: 0.8011 (m-30)
REVERT: B  312 GLU cc_start: 0.8495 (mp0) cc_final: 0.8280 (mp0)
REVERT: B  329 LYS cc_start: 0.8842 (tmtm) cc_final: 0.8624 (tptp)
REVERT: B  354 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8287 (mm-40)
REVERT: B  362 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7952 (mt-10)
REVERT: C   51 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7681 (mtpt)
REVERT: C   84 GLU cc_start: 0.8460 (tt0) cc_final: 0.8251 (tt0)
REVERT: C   96 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7640 (mtt-85)
REVERT: C  100 GLU cc_start: 0.8090 (pm20) cc_final: 0.7888 (pm20)
REVERT: C  122 GLN cc_start: 0.8699 (tt0) cc_final: 0.8487 (tt0)
REVERT: C  148 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7969 (mmt90)
REVERT: C  168 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8392 (mt-10)
REVERT: C  223 ASP cc_start: 0.8301 (t0) cc_final: 0.7973 (t0)
REVERT: C  325 THR cc_start: 0.8732 (m) cc_final: 0.8382 (p)
REVERT: C  355 GLN cc_start: 0.8178 (mm110) cc_final: 0.7872 (mp-120)
  outliers start: 16
  outliers final: 4
  residues processed: 208
  average time/residue: 1.8221
  time to fit residues: 398.8284
Evaluate side-chains
  189 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 183
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  180 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3159 r_free = 0.3159 target = 0.107234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.093658 restraints weight = 10178.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.28
r_work: 0.2828 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8973  Z= 0.276
  Angle     :  0.633   7.944  12162  Z= 0.317
  Chirality :  0.048   0.161   1344
  Planarity :  0.005   0.045   1557
  Dihedral  : 11.736 148.867   1249
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 14.72 %
    Favored  : 81.49 %
  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:  1.65 (0.25), residues: 1107
  helix:  0.98 (0.25), residues: 462
  sheet:  0.93 (0.37), residues: 186
  loop :  1.60 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 341 
 HIS   0.005   0.001   HIS B 162 
 PHE   0.011   0.001   PHE B 263 
 TYR   0.013   0.001   TYR C 295 
 ARG   0.003   0.000   ARG C 291 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 187
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   96 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8010 (mtm-85)
REVERT: A  329 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8349 (tttm)
REVERT: B   29 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7982 (ptp-170)
REVERT: B   58 GLU cc_start: 0.8405 (tt0) cc_final: 0.8160 (tt0)
REVERT: B   73 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7310 (mp0)
REVERT: B  229 LYS cc_start: 0.8031 (mtpm) cc_final: 0.7756 (mttm)
REVERT: B  329 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8572 (tptp)
REVERT: B  354 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8468 (mm-40)
REVERT: B  362 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7916 (mt-10)
REVERT: C   84 GLU cc_start: 0.8555 (tt0) cc_final: 0.8332 (tt0)
REVERT: C   96 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7929 (mtt-85)
REVERT: C  122 GLN cc_start: 0.8877 (tt0) cc_final: 0.8663 (tt0)
REVERT: C  168 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8516 (mt-10)
REVERT: C  223 ASP cc_start: 0.8378 (t0) cc_final: 0.7969 (t0)
REVERT: C  325 THR cc_start: 0.8664 (m) cc_final: 0.8382 (p)
REVERT: C  355 GLN cc_start: 0.8291 (mm110) cc_final: 0.8015 (mp-120)
  outliers start: 36
  outliers final: 13
  residues processed: 204
  average time/residue: 1.5882
  time to fit residues: 339.9407
Evaluate side-chains
  193 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   29 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  352 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0980
   chunk 93 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.111132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.097660 restraints weight = 10429.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.29
r_work: 0.2867 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8973  Z= 0.168
  Angle     :  0.568   7.087  12162  Z= 0.278
  Chirality :  0.045   0.160   1344
  Planarity :  0.004   0.033   1557
  Dihedral  : 11.294 155.100   1240
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.98 %
    Favored  : 81.07 %
  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:  1.89 (0.26), residues: 1107
  helix:  1.20 (0.25), residues: 462
  sheet:  0.93 (0.36), residues: 201
  loop :  1.78 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  80 
 HIS   0.003   0.001   HIS B 162 
 PHE   0.008   0.001   PHE B 256 
 TYR   0.010   0.001   TYR C 295 
 ARG   0.005   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7412 (mp0)
REVERT: A   96 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7995 (mtm-85)
REVERT: A  329 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8354 (tttm)
REVERT: A  360 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7758 (tptm)
REVERT: B   58 GLU cc_start: 0.8325 (tt0) cc_final: 0.8106 (tt0)
REVERT: B   73 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7329 (mp0)
REVERT: B   96 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.8009 (mtm-85)
REVERT: B  229 LYS cc_start: 0.8003 (mtpm) cc_final: 0.7711 (mttp)
REVERT: B  293 ASP cc_start: 0.8332 (m-30) cc_final: 0.8005 (m-30)
REVERT: B  335 GLU cc_start: 0.8490 (pm20) cc_final: 0.8243 (pm20)
REVERT: B  354 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8428 (mm-40)
REVERT: B  362 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7882 (mt-10)
REVERT: C   84 GLU cc_start: 0.8530 (tt0) cc_final: 0.8284 (tt0)
REVERT: C   96 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7929 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8483 (mt-10)
REVERT: C  212 ASP cc_start: 0.8784 (t70) cc_final: 0.8543 (t70)
REVERT: C  223 ASP cc_start: 0.8337 (t0) cc_final: 0.7896 (t0)
REVERT: C  325 THR cc_start: 0.8567 (m) cc_final: 0.8316 (p)
REVERT: C  355 GLN cc_start: 0.8280 (mm110) cc_final: 0.7984 (mp-120)
  outliers start: 28
  outliers final: 14
  residues processed: 203
  average time/residue: 1.6180
  time to fit residues: 344.4935
Evaluate side-chains
  199 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0270
   chunk 15 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.8440

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

Flipped N/Q/H residues before XYZ refinement:
C 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.110494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.097016 restraints weight = 10248.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.28
r_work: 0.2846 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8973  Z= 0.197
  Angle     :  0.583   7.241  12162  Z= 0.285
  Chirality :  0.046   0.162   1344
  Planarity :  0.004   0.035   1557
  Dihedral  : 11.339 158.734   1239
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 15.56 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.26), residues: 1107
  helix:  1.23 (0.25), residues: 462
  sheet:  0.89 (0.36), residues: 201
  loop :  1.77 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  80 
 HIS   0.003   0.001   HIS B 162 
 PHE   0.010   0.001   PHE B 256 
 TYR   0.009   0.001   TYR C 295 
 ARG   0.005   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 180
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.8812 (pp)
REVERT: A   73 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7365 (mp0)
REVERT: A   96 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7990 (mtm-85)
REVERT: A  308 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8158 (mm-30)
REVERT: A  329 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8372 (tttm)
REVERT: A  360 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7707 (tptm)
REVERT: B   58 GLU cc_start: 0.8284 (tt0) cc_final: 0.8072 (tt0)
REVERT: B   96 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.7999 (mtm-85)
REVERT: B  177 MET cc_start: 0.9195 (mmm) cc_final: 0.8553 (mtp)
REVERT: B  229 LYS cc_start: 0.8017 (mtpm) cc_final: 0.7716 (mttt)
REVERT: B  293 ASP cc_start: 0.8306 (m-30) cc_final: 0.8004 (m-30)
REVERT: B  335 GLU cc_start: 0.8484 (pm20) cc_final: 0.8238 (pm20)
REVERT: B  354 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8431 (mm-40)
REVERT: B  362 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7902 (mt-10)
REVERT: C   84 GLU cc_start: 0.8525 (tt0) cc_final: 0.8274 (tt0)
REVERT: C   96 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7961 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8487 (mt-10)
REVERT: C  212 ASP cc_start: 0.8778 (t70) cc_final: 0.8522 (t70)
REVERT: C  223 ASP cc_start: 0.8355 (t0) cc_final: 0.7912 (t0)
REVERT: C  325 THR cc_start: 0.8581 (m) cc_final: 0.8341 (p)
REVERT: C  355 GLN cc_start: 0.8308 (mm110) cc_final: 0.8020 (mp-120)
  outliers start: 36
  outliers final: 17
  residues processed: 197
  average time/residue: 1.5530
  time to fit residues: 321.0144
Evaluate side-chains
  198 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.110761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.097274 restraints weight = 10286.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.28
r_work: 0.2845 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8947
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8973  Z= 0.189
  Angle     :  0.578   7.168  12162  Z= 0.281
  Chirality :  0.046   0.162   1344
  Planarity :  0.004   0.033   1557
  Dihedral  : 11.289 161.092   1239
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.67 %
    Favored  : 81.28 %
  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:  1.92 (0.26), residues: 1107
  helix:  1.27 (0.25), residues: 462
  sheet:  0.90 (0.36), residues: 201
  loop :  1.78 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  80 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.010   0.001   PHE B 256 
 TYR   0.008   0.001   TYR C 295 
 ARG   0.004   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.8807 (pp)
REVERT: A   73 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7382 (mp0)
REVERT: A   96 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7993 (mtm-85)
REVERT: A  216 LYS cc_start: 0.8675 (mptp) cc_final: 0.8464 (tppt)
REVERT: A  329 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8361 (tttm)
REVERT: A  360 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7758 (tptm)
REVERT: B   58 GLU cc_start: 0.8296 (tt0) cc_final: 0.8082 (tt0)
REVERT: B   73 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7426 (mp0)
REVERT: B   96 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7989 (mtm-85)
REVERT: B  229 LYS cc_start: 0.8021 (mtpm) cc_final: 0.7729 (mttt)
REVERT: B  293 ASP cc_start: 0.8301 (m-30) cc_final: 0.8003 (m-30)
REVERT: B  354 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8425 (mm-40)
REVERT: B  362 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7910 (mt-10)
REVERT: C   84 GLU cc_start: 0.8542 (tt0) cc_final: 0.8287 (tt0)
REVERT: C   96 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7983 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8479 (mt-10)
REVERT: C  212 ASP cc_start: 0.8780 (t70) cc_final: 0.8517 (t70)
REVERT: C  223 ASP cc_start: 0.8339 (t0) cc_final: 0.7954 (t0)
REVERT: C  325 THR cc_start: 0.8577 (m) cc_final: 0.8345 (p)
REVERT: C  355 GLN cc_start: 0.8317 (mm110) cc_final: 0.7983 (mp-120)
  outliers start: 29
  outliers final: 19
  residues processed: 191
  average time/residue: 1.6037
  time to fit residues: 321.6332
Evaluate side-chains
  205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3182 r_free = 0.3182 target = 0.108915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.095356 restraints weight = 10271.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.28
r_work: 0.2814 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8972
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8973  Z= 0.274
  Angle     :  0.622   7.642  12162  Z= 0.307
  Chirality :  0.048   0.169   1344
  Planarity :  0.005   0.035   1557
  Dihedral  : 11.509 161.911   1239
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.25 %
    Favored  : 81.28 %
  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:  1.80 (0.26), residues: 1107
  helix:  1.13 (0.25), residues: 462
  sheet:  0.91 (0.36), residues: 201
  loop :  1.72 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 341 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.011   0.001   PHE C 256 
 TYR   0.009   0.001   TYR C 295 
 ARG   0.003   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8806 (pp)
REVERT: A   73 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7383 (mp0)
REVERT: A   96 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7986 (mtm-85)
REVERT: A  216 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8518 (tppt)
REVERT: A  329 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8366 (tttm)
REVERT: A  360 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7732 (tptm)
REVERT: B   58 GLU cc_start: 0.8304 (tt0) cc_final: 0.8088 (tt0)
REVERT: B   73 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7440 (mp0)
REVERT: B  229 LYS cc_start: 0.8044 (mtpm) cc_final: 0.7743 (mttt)
REVERT: B  354 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8478 (mm-40)
REVERT: B  362 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7928 (mt-10)
REVERT: C   84 GLU cc_start: 0.8563 (tt0) cc_final: 0.8318 (tt0)
REVERT: C   96 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7994 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8521 (mt-10)
REVERT: C  212 ASP cc_start: 0.8766 (t70) cc_final: 0.8491 (t70)
REVERT: C  223 ASP cc_start: 0.8399 (t0) cc_final: 0.7997 (t0)
REVERT: C  229 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7851 (mtmt)
REVERT: C  325 THR cc_start: 0.8626 (m) cc_final: 0.8426 (p)
  outliers start: 33
  outliers final: 20
  residues processed: 190
  average time/residue: 1.6793
  time to fit residues: 335.1347
Evaluate side-chains
  200 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 2.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  287 ASP
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3206 r_free = 0.3206 target = 0.110685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.097169 restraints weight = 10347.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.29
r_work: 0.2846 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8973  Z= 0.189
  Angle     :  0.585   7.256  12162  Z= 0.286
  Chirality :  0.046   0.162   1344
  Planarity :  0.004   0.034   1557
  Dihedral  : 11.369 163.738   1239
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.98 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.88 (0.26), residues: 1107
  helix:  1.26 (0.25), residues: 462
  sheet:  0.92 (0.37), residues: 201
  loop :  1.71 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  80 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.009   0.001   PHE B 256 
 TYR   0.009   0.001   TYR B 295 
 ARG   0.006   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.8814 (pp)
REVERT: A   73 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7348 (mp0)
REVERT: A   96 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7984 (mtm-85)
REVERT: A  212 ASP cc_start: 0.8851 (t70) cc_final: 0.8639 (t70)
REVERT: A  216 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8467 (tppt)
REVERT: A  329 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8364 (tttm)
REVERT: A  360 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7767 (tptm)
REVERT: B   58 GLU cc_start: 0.8294 (tt0) cc_final: 0.8075 (tt0)
REVERT: B   73 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7444 (mp0)
REVERT: B  229 LYS cc_start: 0.8039 (mtpm) cc_final: 0.7737 (mttt)
REVERT: B  293 ASP cc_start: 0.8297 (m-30) cc_final: 0.8003 (m-30)
REVERT: B  354 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8401 (mm-40)
REVERT: B  362 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7923 (mt-10)
REVERT: C   84 GLU cc_start: 0.8586 (tt0) cc_final: 0.8332 (tt0)
REVERT: C   96 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7954 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8481 (mt-10)
REVERT: C  212 ASP cc_start: 0.8786 (t70) cc_final: 0.8507 (t70)
REVERT: C  223 ASP cc_start: 0.8357 (t0) cc_final: 0.7965 (t0)
REVERT: C  355 GLN cc_start: 0.8318 (mm110) cc_final: 0.8002 (mp-120)
  outliers start: 29
  outliers final: 17
  residues processed: 193
  average time/residue: 1.5930
  time to fit residues: 322.7133
Evaluate side-chains
  203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0670
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.111172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.097621 restraints weight = 10427.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.30
r_work: 0.2795 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8973  Z= 0.180
  Angle     :  0.583   7.503  12162  Z= 0.283
  Chirality :  0.045   0.161   1344
  Planarity :  0.004   0.041   1557
  Dihedral  : 11.288 166.540   1239
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.40 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.26), residues: 1107
  helix:  1.30 (0.25), residues: 462
  sheet:  0.94 (0.37), residues: 201
  loop :  1.76 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  80 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.009   0.001   PHE B 256 
 TYR   0.008   0.001   TYR B 295 
 ARG   0.009   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8794 (pp)
REVERT: A   73 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7376 (mp0)
REVERT: A   96 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7962 (mtm-85)
REVERT: A  216 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8496 (tppt)
REVERT: A  329 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8413 (tttm)
REVERT: A  360 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7701 (tptm)
REVERT: B   58 GLU cc_start: 0.8305 (tt0) cc_final: 0.8061 (tt0)
REVERT: B   73 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7417 (mp0)
REVERT: B  229 LYS cc_start: 0.7997 (mtpm) cc_final: 0.7689 (mttt)
REVERT: B  293 ASP cc_start: 0.8318 (m-30) cc_final: 0.8006 (m-30)
REVERT: B  362 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7876 (mt-10)
REVERT: C   41 ASN cc_start: 0.8153 (m110) cc_final: 0.7926 (m110)
REVERT: C   84 GLU cc_start: 0.8593 (tt0) cc_final: 0.8368 (tt0)
REVERT: C   96 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7951 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8505 (mt-10)
REVERT: C  212 ASP cc_start: 0.8772 (t70) cc_final: 0.8487 (t70)
REVERT: C  223 ASP cc_start: 0.8350 (t0) cc_final: 0.7934 (t0)
REVERT: C  229 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7789 (mtmt)
REVERT: C  355 GLN cc_start: 0.8312 (mm110) cc_final: 0.7994 (mp-120)
  outliers start: 28
  outliers final: 18
  residues processed: 198
  average time/residue: 1.4661
  time to fit residues: 305.4084
Evaluate side-chains
  205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0570
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
C  13 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.111758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.098277 restraints weight = 10311.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.29
r_work: 0.2883 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8973  Z= 0.170
  Angle     :  0.579   7.935  12162  Z= 0.280
  Chirality :  0.045   0.159   1344
  Planarity :  0.004   0.041   1557
  Dihedral  : 11.150 169.414   1239
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.61 %
    Favored  : 80.44 %
  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:  1.99 (0.26), residues: 1107
  helix:  1.36 (0.25), residues: 462
  sheet:  0.94 (0.37), residues: 201
  loop :  1.77 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  80 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.009   0.001   PHE B 256 
 TYR   0.008   0.001   TYR B 295 
 ARG   0.010   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 1.061 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.8807 (pp)
REVERT: A   73 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7379 (mp0)
REVERT: A   96 ARG cc_start: 0.8305 (mtp85) cc_final: 0.8001 (mtm-85)
REVERT: A  216 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8496 (tppt)
REVERT: A  329 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8391 (tttm)
REVERT: A  360 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7797 (tptm)
REVERT: B   58 GLU cc_start: 0.8304 (tt0) cc_final: 0.8070 (tt0)
REVERT: B   73 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7452 (mp0)
REVERT: B  229 LYS cc_start: 0.8046 (mtpm) cc_final: 0.7758 (mttt)
REVERT: B  362 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7927 (mt-10)
REVERT: C   41 ASN cc_start: 0.8161 (m110) cc_final: 0.7925 (m110)
REVERT: C   84 GLU cc_start: 0.8572 (tt0) cc_final: 0.8284 (mt-10)
REVERT: C   96 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7949 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8464 (mt-10)
REVERT: C  212 ASP cc_start: 0.8772 (t70) cc_final: 0.8502 (t70)
REVERT: C  223 ASP cc_start: 0.8345 (t0) cc_final: 0.7953 (t0)
REVERT: C  229 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7887 (mtmt)
REVERT: C  355 GLN cc_start: 0.8324 (mm110) cc_final: 0.8005 (mp-120)
  outliers start: 28
  outliers final: 18
  residues processed: 190
  average time/residue: 1.5792
  time to fit residues: 315.1689
Evaluate side-chains
  204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0870
   chunk 29 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0870
   chunk 102 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4536

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.113226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.099882 restraints weight = 10383.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.28
r_work: 0.2915 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8973  Z= 0.148
  Angle     :  0.571   8.261  12162  Z= 0.274
  Chirality :  0.045   0.157   1344
  Planarity :  0.004   0.041   1557
  Dihedral  : 10.909 174.052   1239
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.35 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.08 (0.26), residues: 1107
  helix:  1.45 (0.25), residues: 462
  sheet:  0.98 (0.37), residues: 201
  loop :  1.80 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  80 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.008   0.001   PHE B 256 
 TYR   0.008   0.001   TYR B 295 
 ARG   0.010   0.000   ARG B  96 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   65 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.8794 (pp)
REVERT: A   73 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7372 (mp0)
REVERT: A  216 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (tppt)
REVERT: A  329 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8374 (tttm)
REVERT: A  360 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7789 (tptm)
REVERT: B   58 GLU cc_start: 0.8286 (tt0) cc_final: 0.8086 (tt0)
REVERT: B   73 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7465 (mp0)
REVERT: B  229 LYS cc_start: 0.8053 (mtpm) cc_final: 0.7767 (mttt)
REVERT: B  277 ARG cc_start: 0.8814 (mmt180) cc_final: 0.8505 (tpt170)
REVERT: B  362 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: C   41 ASN cc_start: 0.8168 (m110) cc_final: 0.7938 (m110)
REVERT: C   84 GLU cc_start: 0.8562 (tt0) cc_final: 0.8276 (mt-10)
REVERT: C   96 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7936 (mtt-85)
REVERT: C  168 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8443 (mt-10)
REVERT: C  212 ASP cc_start: 0.8748 (t70) cc_final: 0.8457 (t70)
REVERT: C  223 ASP cc_start: 0.8327 (t0) cc_final: 0.7945 (t0)
REVERT: C  229 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7887 (mtmt)
REVERT: C  355 GLN cc_start: 0.8290 (mm110) cc_final: 0.7976 (mp-120)
  outliers start: 24
  outliers final: 15
  residues processed: 192
  average time/residue: 2.0420
  time to fit residues: 411.2968
Evaluate side-chains
  201 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 2.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  360 LYS
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue    7 GLN
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  292 LYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  366 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    0.0970
   chunk 98 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3205 r_free = 0.3205 target = 0.110667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.097125 restraints weight = 10442.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.30
r_work: 0.2853 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8954
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8973  Z= 0.213
  Angle     :  0.609   8.432  12162  Z= 0.297
  Chirality :  0.046   0.161   1344
  Planarity :  0.004   0.041   1557
  Dihedral  : 11.127 171.853   1239
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.56 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.99 (0.26), residues: 1107
  helix:  1.30 (0.25), residues: 462
  sheet:  1.04 (0.37), residues: 198
  loop :  1.77 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  80 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.010   0.001   PHE B 256 
 TYR   0.008   0.001   TYR B 295 
 ARG   0.009   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8167.65 seconds
wall clock time: 141 minutes 19.12 seconds (8479.12 seconds total)