Starting phenix.real_space_refine
on Tue Jan 14 19:00:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bxr_45009/01_2025/9bxr_45009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bxr_45009/01_2025/9bxr_45009.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bxr_45009/01_2025/9bxr_45009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bxr_45009/01_2025/9bxr_45009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bxr_45009/01_2025/9bxr_45009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bxr_45009/01_2025/9bxr_45009.cif"
  }
  resolution = 3.2
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2202      2.51       5
     N     648      2.21       5
     O     672      1.98       5
     H    3656      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7184
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1198
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 1198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1198
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "G"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "E"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "H"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1197
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Time building chain proxies: 3.84, per 1000 atoms: 0.53
  Number of scatterers: 7184
  At special positions: 0
  Unit cell: (134.274, 107.586, 39.198, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     672      8.00
     N     648      7.00
     C    2202      6.00
     H    3656      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 566.3 milliseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  804

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 15 sheets defined
      0.0% alpha, 25.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 7.064A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   VAL D 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.617A  pdb=" N   LYS D 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   SER E 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   THR D 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.784A  pdb=" N   CYS E 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LYS D 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340
    Processing sheet with id=AA5, first strand: chain 'C' and resid 358 through 359
      removed outlier: 6.305A  pdb=" N   ASP C 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ASP D 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 369 through 373
      removed outlier: 7.037A  pdb=" N   LYS C 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   GLU D 372 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE C 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   LYS D 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.336A  pdb=" N   GLU E 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE D 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'F' and resid 306 through 310
      removed outlier: 6.546A  pdb=" N   GLN F 307 " --> pdb=" O   ILE G 308 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   TYR G 310 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   VAL F 309 " --> pdb=" O   TYR G 310 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   GLN G 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   TYR H 310 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL G 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 313 through 314
      removed outlier: 6.748A  pdb=" N   VAL F 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   VAL G 313 " --> pdb=" O   ASP H 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'F' and resid 317 through 318
      removed outlier: 6.372A  pdb=" N   LYS F 317 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LYS G 317 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 328 through 330
    Processing sheet with id=AB2, first strand: chain 'F' and resid 336 through 340
    Processing sheet with id=AB3, first strand: chain 'F' and resid 343 through 346
    Processing sheet with id=AB4, first strand: chain 'F' and resid 356 through 358
    Processing sheet with id=AB5, first strand: chain 'F' and resid 361 through 362
    Processing sheet with id=AB6, first strand: chain 'F' and resid 369 through 371

    49 hydrogen bonds defined for protein.
    147 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: 2.13

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3650
        1.12 -     1.29: 600
        1.29 -     1.46: 1007
        1.46 -     1.64: 1975
        1.64 -     1.81: 6
  Bond restraints: 7238
  Sorted by residual:
  bond pdb=" NE2 GLN E 307 "
       pdb="HE21 GLN E 307 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" N   GLU E 338 "
       pdb=" H   GLU E 338 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   LEU G 357 "
       pdb=" H   LEU G 357 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" CE1 HIS G 362 "
       pdb=" HE1 HIS G 362 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   LEU H 357 "
       pdb=" H   LEU H 357 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 7233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 10877
        2.42 -     4.83: 1806
        4.83 -     7.25: 446
        7.25 -     9.66: 57
        9.66 -    12.08: 6
  Bond angle restraints: 13192
  Sorted by residual:
  angle pdb=" CA  ASP G 348 "
        pdb=" CB  ASP G 348 "
        pdb=" CG  ASP G 348 "
      ideal   model   delta    sigma   weight residual
     112.60  117.21   -4.61 1.00e+00 1.00e+00 2.12e+01
  angle pdb=" CA  ASP F 348 "
        pdb=" CB  ASP F 348 "
        pdb=" CG  ASP F 348 "
      ideal   model   delta    sigma   weight residual
     112.60  117.21   -4.61 1.00e+00 1.00e+00 2.12e+01
  angle pdb=" CA  ASP H 348 "
        pdb=" CB  ASP H 348 "
        pdb=" CG  ASP H 348 "
      ideal   model   delta    sigma   weight residual
     112.60  117.17   -4.57 1.00e+00 1.00e+00 2.09e+01
  angle pdb=" CB  HIS H 329 "
        pdb=" CG  HIS H 329 "
        pdb=" CD2 HIS H 329 "
      ideal   model   delta    sigma   weight residual
     131.20  125.34    5.86 1.30e+00 5.92e-01 2.03e+01
  angle pdb=" CB  HIS G 329 "
        pdb=" CG  HIS G 329 "
        pdb=" CD2 HIS G 329 "
      ideal   model   delta    sigma   weight residual
     131.20  125.35    5.85 1.30e+00 5.92e-01 2.03e+01
  ... (remaining 13187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 2934
       16.79 -    33.58: 241
       33.58 -    50.37: 37
       50.37 -    67.16: 111
       67.16 -    83.96: 3
  Dihedral angle restraints: 3326
    sinusoidal: 1902
      harmonic: 1424
  Sorted by residual:
  dihedral pdb=" CA  ILE H 360 "
           pdb=" C   ILE H 360 "
           pdb=" N   THR H 361 "
           pdb=" CA  THR H 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.96   24.04     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  ILE F 360 "
           pdb=" C   ILE F 360 "
           pdb=" N   THR F 361 "
           pdb=" CA  THR F 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.00   24.00     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  ILE G 360 "
           pdb=" C   ILE G 360 "
           pdb=" N   THR G 361 "
           pdb=" CA  THR G 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.00   24.00     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 3323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 275
       0.065 -    0.129: 200
       0.129 -    0.193: 53
       0.193 -    0.257: 0
       0.257 -    0.322: 6
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  GLU D 380 "
            pdb=" N   GLU D 380 "
            pdb=" C   GLU D 380 "
            pdb=" CB  GLU D 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  GLU C 380 "
            pdb=" N   GLU C 380 "
            pdb=" C   GLU C 380 "
            pdb=" CB  GLU C 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  GLU E 380 "
            pdb=" N   GLU E 380 "
            pdb=" C   GLU E 380 "
            pdb=" CB  GLU E 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 531 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G 346 "   -0.085 2.00e-02 2.50e+03   3.30e-02 3.27e+01
        pdb=" CG  PHE G 346 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE G 346 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 PHE G 346 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 PHE G 346 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE G 346 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE G 346 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 PHE G 346 "    0.009 2.00e-02 2.50e+03
        pdb=" HD2 PHE G 346 "    0.020 2.00e-02 2.50e+03
        pdb=" HE1 PHE G 346 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 PHE G 346 "   -0.009 2.00e-02 2.50e+03
        pdb=" HZ  PHE G 346 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F 346 "   -0.085 2.00e-02 2.50e+03   3.30e-02 3.27e+01
        pdb=" CG  PHE F 346 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE F 346 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 PHE F 346 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 PHE F 346 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE F 346 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE F 346 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 PHE F 346 "    0.009 2.00e-02 2.50e+03
        pdb=" HD2 PHE F 346 "    0.020 2.00e-02 2.50e+03
        pdb=" HE1 PHE F 346 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE2 PHE F 346 "   -0.008 2.00e-02 2.50e+03
        pdb=" HZ  PHE F 346 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 346 "   -0.085 2.00e-02 2.50e+03   3.30e-02 3.26e+01
        pdb=" CG  PHE H 346 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 346 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 346 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 346 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 346 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 346 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 PHE H 346 "    0.009 2.00e-02 2.50e+03
        pdb=" HD2 PHE H 346 "    0.020 2.00e-02 2.50e+03
        pdb=" HE1 PHE H 346 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE H 346 "   -0.008 2.00e-02 2.50e+03
        pdb=" HZ  PHE H 346 "   -0.042 2.00e-02 2.50e+03
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        0.32 -     1.18: 20
        1.18 -     2.03: 339
        2.03 -     2.89: 16323
        2.89 -     3.74: 29034
        3.74 -     4.60: 46232
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 91948
  Sorted by model distance:
  nonbonded pdb=" HG  SER G 352 "
            pdb=" O   SER H 352 "
     model   vdw
     0.322 2.450
  nonbonded pdb=" HG  SER F 352 "
            pdb=" O   SER G 352 "
     model   vdw
     0.363 2.450
  nonbonded pdb="HD23 LEU C 325 "
            pdb="HD11 LEU D 325 "
     model   vdw
     0.718 2.440
  nonbonded pdb="HD23 LEU D 325 "
            pdb="HD11 LEU E 325 "
     model   vdw
     0.768 2.440
  nonbonded pdb=" HA  ILE G 354 "
            pdb="HD13 ILE H 354 "
     model   vdw
     0.797 2.440
  ... (remaining 91943 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 304 through 329 or (resid 330 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ 
 NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ 
e HE2)) or resid 331 through 380))
  selection = (chain 'D' and (resid 304 through 329 or (resid 330 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ 
 NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ 
e HE2)) or resid 331 through 380))
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:             2.590
  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:             0.120
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.040
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.042   3582  Z= 0.782
  Angle     :  1.867   6.584   4794  Z= 1.214
  Chirality :  0.087   0.322    534
  Planarity :  0.008   0.035    618
  Dihedral  : 11.163  83.955   1380
  Min Nonbonded Distance : 0.991

Molprobity Statistics.
  All-atom Clashscore : 32.81
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  :  6.67 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  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: -2.61 (0.28), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.21), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.003   HIS G 362 
 PHE   0.058   0.012   PHE F 346 
 TYR   0.057   0.021   TYR D 310 
 ARG   0.001   0.000   ARG H 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6385 (mp0) cc_final: 0.6061 (mp0)
REVERT: C  369 LYS cc_start: 0.8214 (pttt) cc_final: 0.7940 (ptpt)
REVERT: F  337 VAL cc_start: 0.7330 (t) cc_final: 0.6935 (t)
REVERT: F  338 GLU cc_start: 0.6578 (mp0) cc_final: 0.6244 (mp0)
REVERT: F  379 ARG cc_start: 0.6781 (ptp-170) cc_final: 0.5941 (ptm160)
REVERT: D  353 LYS cc_start: 0.7642 (mttt) cc_final: 0.7149 (mmtm)
REVERT: D  369 LYS cc_start: 0.8059 (pttt) cc_final: 0.7749 (ptpt)
REVERT: G  336 GLN cc_start: 0.6780 (mt0) cc_final: 0.5728 (mp-120)
REVERT: G  337 VAL cc_start: 0.7166 (t) cc_final: 0.6504 (t)
REVERT: G  338 GLU cc_start: 0.6400 (mp0) cc_final: 0.5362 (mp0)
REVERT: G  340 LYS cc_start: 0.6194 (mmtm) cc_final: 0.5795 (tptp)
REVERT: G  372 GLU cc_start: 0.8434 (tt0) cc_final: 0.8077 (mt-10)
REVERT: G  379 ARG cc_start: 0.6391 (ptp-170) cc_final: 0.6026 (ptm-80)
REVERT: E  317 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7478 (ptpp)
REVERT: E  353 LYS cc_start: 0.7563 (mttt) cc_final: 0.7154 (mmtm)
REVERT: E  369 LYS cc_start: 0.8144 (pttt) cc_final: 0.7885 (ptpt)
REVERT: E  380 GLU cc_start: 0.5194 (tt0) cc_final: 0.4186 (mp0)
REVERT: H  337 VAL cc_start: 0.6658 (t) cc_final: 0.6282 (p)
REVERT: H  338 GLU cc_start: 0.6568 (mp0) cc_final: 0.6302 (mp0)
REVERT: H  353 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7176 (mttp)
REVERT: H  372 GLU cc_start: 0.8377 (tt0) cc_final: 0.7818 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.6212
  time to fit residues: 73.2949
Evaluate side-chains
  79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
F 330 HIS
G 327 ASN
G 330 HIS
** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.179304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.143502 restraints weight = 11904.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 2.44
r_work: 0.4266 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4165 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3582  Z= 0.243
  Angle     :  0.703   5.317   4794  Z= 0.373
  Chirality :  0.050   0.130    534
  Planarity :  0.003   0.021    618
  Dihedral  :  9.197  76.537    480
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  7.71 %
    Favored  : 90.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.27), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.21), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.018   0.003   PHE H 346 
 TYR   0.017   0.003   TYR D 310 
 ARG   0.003   0.001   ARG E 349 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6127 (mp0) cc_final: 0.5615 (mp0)
REVERT: C  369 LYS cc_start: 0.8380 (pttt) cc_final: 0.8176 (ptpt)
REVERT: F  372 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8110 (mt-10)
REVERT: F  379 ARG cc_start: 0.7171 (ptp-170) cc_final: 0.6392 (ptm160)
REVERT: F  380 GLU cc_start: 0.7077 (tt0) cc_final: 0.5914 (pm20)
REVERT: D  314 ASP cc_start: 0.7743 (m-30) cc_final: 0.7479 (t70)
REVERT: G  311 LYS cc_start: 0.8502 (mttt) cc_final: 0.8228 (tmtt)
REVERT: G  337 VAL cc_start: 0.7237 (t) cc_final: 0.6655 (t)
REVERT: G  338 GLU cc_start: 0.6476 (mp0) cc_final: 0.5742 (mp0)
REVERT: G  340 LYS cc_start: 0.6447 (mmtm) cc_final: 0.6114 (tptp)
REVERT: G  372 GLU cc_start: 0.8410 (tt0) cc_final: 0.8023 (mt-10)
REVERT: G  379 ARG cc_start: 0.6762 (ptp-170) cc_final: 0.6215 (ptm-80)
REVERT: E  314 ASP cc_start: 0.7798 (m-30) cc_final: 0.7456 (t0)
REVERT: E  317 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7789 (ptpp)
REVERT: E  368 ASN cc_start: 0.7968 (m-40) cc_final: 0.7617 (m-40)
REVERT: E  369 LYS cc_start: 0.8350 (pttt) cc_final: 0.8134 (ptpt)
REVERT: E  375 LYS cc_start: 0.8153 (tttt) cc_final: 0.7782 (mttm)
REVERT: H  311 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8378 (mttt)
REVERT: H  337 VAL cc_start: 0.6631 (t) cc_final: 0.6341 (t)
REVERT: H  338 GLU cc_start: 0.6466 (mp0) cc_final: 0.6197 (mp0)
REVERT: H  351 GLN cc_start: 0.6659 (pt0) cc_final: 0.5698 (pm20)
REVERT: H  369 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8021 (tttt)
REVERT: H  372 GLU cc_start: 0.8272 (tt0) cc_final: 0.7851 (mt-10)
REVERT: H  379 ARG cc_start: 0.6464 (ptp-170) cc_final: 0.6249 (ptp90)
  outliers start: 7
  outliers final: 3
  residues processed: 95
  average time/residue: 0.5293
  time to fit residues: 57.4790
Evaluate side-chains
  80 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
G 307 GLN
G 359 ASN
** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.174547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.140721 restraints weight = 12652.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4304 rms_B_bonded: 2.41
r_work: 0.4235 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4137 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3582  Z= 0.227
  Angle     :  0.621   4.738   4794  Z= 0.324
  Chirality :  0.050   0.130    534
  Planarity :  0.003   0.025    618
  Dihedral  :  8.223  65.258    480
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.45 %
    Favored  : 86.82 %
  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: -2.84 (0.28), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.21), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 329 
 PHE   0.013   0.002   PHE H 346 
 TYR   0.016   0.003   TYR C 310 
 ARG   0.002   0.000   ARG G 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6365 (mp0) cc_final: 0.5982 (mp0)
REVERT: C  369 LYS cc_start: 0.8412 (pttt) cc_final: 0.8179 (ptpt)
REVERT: F  311 LYS cc_start: 0.8578 (tptt) cc_final: 0.8127 (tptm)
REVERT: F  372 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8103 (mt-10)
REVERT: F  379 ARG cc_start: 0.7160 (ptp-170) cc_final: 0.6495 (ptm160)
REVERT: F  380 GLU cc_start: 0.7140 (tt0) cc_final: 0.6073 (pm20)
REVERT: G  337 VAL cc_start: 0.7335 (t) cc_final: 0.6757 (t)
REVERT: G  338 GLU cc_start: 0.6631 (mp0) cc_final: 0.5870 (mp0)
REVERT: G  340 LYS cc_start: 0.6577 (mmtm) cc_final: 0.6279 (tmtt)
REVERT: G  372 GLU cc_start: 0.8442 (tt0) cc_final: 0.8177 (mt-10)
REVERT: E  317 LYS cc_start: 0.8388 (ptmt) cc_final: 0.7797 (ptpp)
REVERT: E  368 ASN cc_start: 0.7979 (m-40) cc_final: 0.7654 (m-40)
REVERT: E  369 LYS cc_start: 0.8316 (pttt) cc_final: 0.8069 (ptpp)
REVERT: E  375 LYS cc_start: 0.8116 (tttt) cc_final: 0.7787 (mttm)
REVERT: H  328 ILE cc_start: 0.8336 (mt) cc_final: 0.8074 (mp)
REVERT: H  337 VAL cc_start: 0.6947 (t) cc_final: 0.6606 (t)
REVERT: H  338 GLU cc_start: 0.6663 (mp0) cc_final: 0.6426 (mp0)
REVERT: H  372 GLU cc_start: 0.8244 (tt0) cc_final: 0.7870 (mt-10)
  outliers start: 11
  outliers final: 7
  residues processed: 89
  average time/residue: 0.5428
  time to fit residues: 54.5816
Evaluate side-chains
  81 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain D residue  317 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain G residue  359 ASN
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 4 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
G 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.170595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.136777 restraints weight = 12933.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 2.48
r_work: 0.4190 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4090 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3582  Z= 0.320
  Angle     :  0.657   5.262   4794  Z= 0.342
  Chirality :  0.050   0.132    534
  Planarity :  0.003   0.031    618
  Dihedral  :  8.155  64.405    480
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 11.19 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F 329 
 PHE   0.013   0.002   PHE H 346 
 TYR   0.018   0.003   TYR E 310 
 ARG   0.002   0.000   ARG G 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6209 (mp0) cc_final: 0.5781 (mp0)
REVERT: C  369 LYS cc_start: 0.8436 (pttt) cc_final: 0.8166 (ptpt)
REVERT: F  311 LYS cc_start: 0.8625 (tptt) cc_final: 0.8047 (tppt)
REVERT: F  372 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8208 (mt-10)
REVERT: F  379 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6462 (ptm160)
REVERT: F  380 GLU cc_start: 0.7127 (tt0) cc_final: 0.6037 (pm20)
REVERT: G  311 LYS cc_start: 0.8432 (tttt) cc_final: 0.7789 (tptp)
REVERT: G  319 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8212 (p)
REVERT: G  337 VAL cc_start: 0.7173 (t) cc_final: 0.6664 (t)
REVERT: G  338 GLU cc_start: 0.6638 (mp0) cc_final: 0.5824 (mp0)
REVERT: G  340 LYS cc_start: 0.6321 (mmtm) cc_final: 0.6089 (tmtt)
REVERT: G  372 GLU cc_start: 0.8498 (tt0) cc_final: 0.8231 (mt-10)
REVERT: E  317 LYS cc_start: 0.8400 (ptmt) cc_final: 0.7744 (ptpp)
REVERT: E  327 ASN cc_start: 0.8367 (p0) cc_final: 0.8139 (p0)
REVERT: E  368 ASN cc_start: 0.7938 (m-40) cc_final: 0.7581 (m-40)
REVERT: E  369 LYS cc_start: 0.8405 (pttt) cc_final: 0.8077 (ptpp)
REVERT: E  375 LYS cc_start: 0.8161 (tttt) cc_final: 0.7829 (mttm)
REVERT: H  328 ILE cc_start: 0.8232 (mt) cc_final: 0.7988 (mp)
REVERT: H  337 VAL cc_start: 0.6927 (t) cc_final: 0.6566 (t)
REVERT: H  338 GLU cc_start: 0.6631 (mp0) cc_final: 0.6402 (mp0)
REVERT: H  369 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8099 (tttt)
  outliers start: 12
  outliers final: 7
  residues processed: 89
  average time/residue: 0.5369
  time to fit residues: 54.8236
Evaluate side-chains
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain D residue  317 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.176305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.142604 restraints weight = 12375.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.4333 rms_B_bonded: 2.42
r_work: 0.4260 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4161 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3582  Z= 0.144
  Angle     :  0.525   3.877   4794  Z= 0.267
  Chirality :  0.048   0.127    534
  Planarity :  0.003   0.028    618
  Dihedral  :  7.774  69.602    480
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.19 %
    Favored  : 85.57 %
  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: -2.79 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G 330 
 PHE   0.005   0.001   PHE H 346 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.001   0.000   ARG H 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6068 (mp0) cc_final: 0.5651 (mp0)
REVERT: C  369 LYS cc_start: 0.8455 (pttt) cc_final: 0.8167 (ptpt)
REVERT: F  311 LYS cc_start: 0.8521 (tptt) cc_final: 0.7895 (tppt)
REVERT: F  372 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8214 (mt-10)
REVERT: F  380 GLU cc_start: 0.7047 (tt0) cc_final: 0.6060 (pm20)
REVERT: G  311 LYS cc_start: 0.8376 (tttt) cc_final: 0.7716 (tptp)
REVERT: G  337 VAL cc_start: 0.7207 (t) cc_final: 0.6858 (t)
REVERT: G  338 GLU cc_start: 0.6697 (mp0) cc_final: 0.5995 (mp0)
REVERT: G  340 LYS cc_start: 0.6358 (mmtm) cc_final: 0.6032 (tmtt)
REVERT: G  372 GLU cc_start: 0.8506 (tt0) cc_final: 0.8229 (mt-10)
REVERT: E  317 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7716 (ptpp)
REVERT: E  368 ASN cc_start: 0.8061 (m-40) cc_final: 0.7737 (m-40)
REVERT: E  369 LYS cc_start: 0.8404 (pttt) cc_final: 0.7824 (ptmm)
REVERT: E  375 LYS cc_start: 0.8049 (tttt) cc_final: 0.7689 (mttm)
REVERT: H  328 ILE cc_start: 0.8193 (mt) cc_final: 0.7956 (mp)
REVERT: H  338 GLU cc_start: 0.6668 (mp0) cc_final: 0.6465 (mp0)
REVERT: H  372 GLU cc_start: 0.8321 (tt0) cc_final: 0.7899 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 91
  average time/residue: 0.5139
  time to fit residues: 53.5895
Evaluate side-chains
  83 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.4645 r_free = 0.4645 target = 0.173014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.139401 restraints weight = 12668.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.4290 rms_B_bonded: 2.37
r_work: 0.4217 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.4116 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.5440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3582  Z= 0.232
  Angle     :  0.575   4.897   4794  Z= 0.294
  Chirality :  0.049   0.127    534
  Planarity :  0.003   0.032    618
  Dihedral  :  7.620  65.781    480
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.18 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.87 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 329 
 PHE   0.009   0.002   PHE G 346 
 TYR   0.015   0.003   TYR E 310 
 ARG   0.001   0.000   ARG H 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6088 (mp0) cc_final: 0.5665 (mp0)
REVERT: C  369 LYS cc_start: 0.8465 (pttt) cc_final: 0.8179 (ptpt)
REVERT: F  311 LYS cc_start: 0.8550 (tptt) cc_final: 0.7947 (tppt)
REVERT: F  372 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: F  380 GLU cc_start: 0.7013 (tt0) cc_final: 0.6057 (pm20)
REVERT: D  349 ARG cc_start: 0.6736 (mtp180) cc_final: 0.5905 (mtt90)
REVERT: G  311 LYS cc_start: 0.8381 (tttt) cc_final: 0.7770 (tptp)
REVERT: G  337 VAL cc_start: 0.7192 (t) cc_final: 0.6879 (t)
REVERT: G  338 GLU cc_start: 0.6744 (mp0) cc_final: 0.5998 (mp0)
REVERT: G  340 LYS cc_start: 0.6357 (mmtm) cc_final: 0.6013 (tmtt)
REVERT: G  372 GLU cc_start: 0.8486 (tt0) cc_final: 0.8182 (mt-10)
REVERT: E  317 LYS cc_start: 0.8401 (ptmt) cc_final: 0.7748 (ptpp)
REVERT: E  342 GLU cc_start: 0.3221 (pm20) cc_final: 0.1894 (mt-10)
REVERT: E  368 ASN cc_start: 0.8058 (m-40) cc_final: 0.7726 (m-40)
REVERT: E  369 LYS cc_start: 0.8401 (pttt) cc_final: 0.8119 (ptpp)
REVERT: E  375 LYS cc_start: 0.8085 (tttt) cc_final: 0.7742 (mttm)
REVERT: H  328 ILE cc_start: 0.8219 (mt) cc_final: 0.7992 (mp)
REVERT: H  338 GLU cc_start: 0.6773 (mp0) cc_final: 0.6459 (mp0)
REVERT: H  369 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8009 (tttt)
REVERT: H  372 GLU cc_start: 0.8343 (tt0) cc_final: 0.8031 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 89
  average time/residue: 0.5595
  time to fit residues: 56.6172
Evaluate side-chains
  86 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain D residue  317 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4677 r_free = 0.4677 target = 0.176304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.142612 restraints weight = 12412.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 2.42
r_work: 0.4262 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4163 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.5665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3582  Z= 0.153
  Angle     :  0.513   3.825   4794  Z= 0.261
  Chirality :  0.048   0.128    534
  Planarity :  0.003   0.032    618
  Dihedral  :  7.407  68.153    480
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.93 %
    Favored  : 83.33 %
  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: -2.76 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 330 
 PHE   0.005   0.001   PHE H 346 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.002   0.000   ARG H 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6045 (mp0) cc_final: 0.5653 (mp0)
REVERT: C  369 LYS cc_start: 0.8501 (pttt) cc_final: 0.8196 (ptpt)
REVERT: F  311 LYS cc_start: 0.8515 (tptt) cc_final: 0.7879 (tppt)
REVERT: F  372 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8195 (mt-10)
REVERT: F  380 GLU cc_start: 0.6989 (tt0) cc_final: 0.6008 (pm20)
REVERT: D  349 ARG cc_start: 0.6633 (mtp180) cc_final: 0.5819 (mtt90)
REVERT: G  311 LYS cc_start: 0.8382 (tttt) cc_final: 0.7731 (tptp)
REVERT: G  338 GLU cc_start: 0.6757 (mp0) cc_final: 0.6015 (mp0)
REVERT: G  340 LYS cc_start: 0.6250 (mmtm) cc_final: 0.5923 (tmtt)
REVERT: G  372 GLU cc_start: 0.8521 (tt0) cc_final: 0.8240 (mt-10)
REVERT: E  317 LYS cc_start: 0.8397 (ptmt) cc_final: 0.7715 (ptpp)
REVERT: E  342 GLU cc_start: 0.3133 (pm20) cc_final: 0.2436 (pm20)
REVERT: E  368 ASN cc_start: 0.7963 (m-40) cc_final: 0.7647 (m-40)
REVERT: E  369 LYS cc_start: 0.8405 (pttt) cc_final: 0.8095 (ptpp)
REVERT: E  375 LYS cc_start: 0.8020 (tttt) cc_final: 0.7666 (mttm)
REVERT: H  328 ILE cc_start: 0.8203 (mt) cc_final: 0.7972 (mp)
REVERT: H  338 GLU cc_start: 0.6758 (mp0) cc_final: 0.6452 (mp0)
REVERT: H  369 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8008 (tttt)
REVERT: H  372 GLU cc_start: 0.8349 (tt0) cc_final: 0.7946 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.5317
  time to fit residues: 53.6882
Evaluate side-chains
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.4649 r_free = 0.4649 target = 0.173788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.140376 restraints weight = 12654.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 2.41
r_work: 0.4235 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4135 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.5736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3582  Z= 0.207
  Angle     :  0.547   4.472   4794  Z= 0.278
  Chirality :  0.048   0.129    534
  Planarity :  0.003   0.035    618
  Dihedral  :  7.317  65.024    480
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.68 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.81 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 329 
 PHE   0.008   0.002   PHE G 346 
 TYR   0.014   0.002   TYR E 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6075 (mp0) cc_final: 0.5674 (mp0)
REVERT: C  369 LYS cc_start: 0.8470 (pttt) cc_final: 0.8249 (ptpt)
REVERT: F  311 LYS cc_start: 0.8526 (tptt) cc_final: 0.7893 (tppt)
REVERT: F  372 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8198 (mt-10)
REVERT: F  380 GLU cc_start: 0.6942 (tt0) cc_final: 0.6009 (pm20)
REVERT: D  316 SER cc_start: 0.9183 (p) cc_final: 0.8798 (m)
REVERT: D  349 ARG cc_start: 0.6652 (mtp180) cc_final: 0.5839 (mtt90)
REVERT: G  311 LYS cc_start: 0.8359 (tttt) cc_final: 0.7723 (tptp)
REVERT: G  319 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (p)
REVERT: G  338 GLU cc_start: 0.6627 (mp0) cc_final: 0.5826 (mp0)
REVERT: G  340 LYS cc_start: 0.6178 (mmtm) cc_final: 0.5836 (tmtt)
REVERT: G  372 GLU cc_start: 0.8543 (tt0) cc_final: 0.8326 (mt-10)
REVERT: E  317 LYS cc_start: 0.8394 (ptmt) cc_final: 0.7704 (ptpp)
REVERT: E  342 GLU cc_start: 0.3238 (pm20) cc_final: 0.2249 (pm20)
REVERT: E  368 ASN cc_start: 0.8041 (m-40) cc_final: 0.7708 (m-40)
REVERT: E  369 LYS cc_start: 0.8420 (pttt) cc_final: 0.8112 (ptpp)
REVERT: E  375 LYS cc_start: 0.8064 (tttt) cc_final: 0.7719 (mttm)
REVERT: H  328 ILE cc_start: 0.8156 (mt) cc_final: 0.7927 (mp)
REVERT: H  338 GLU cc_start: 0.6726 (mp0) cc_final: 0.6434 (mp0)
REVERT: H  369 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8048 (tttt)
  outliers start: 9
  outliers final: 7
  residues processed: 87
  average time/residue: 0.4488
  time to fit residues: 44.8721
Evaluate side-chains
  88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Chi-restraints excluded: chain H residue  361 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4665 r_free = 0.4665 target = 0.175535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.142157 restraints weight = 12458.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.4339 rms_B_bonded: 2.41
r_work: 0.4264 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4164 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.5865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3582  Z= 0.152
  Angle     :  0.504   3.811   4794  Z= 0.256
  Chirality :  0.048   0.126    534
  Planarity :  0.003   0.036    618
  Dihedral  :  7.164  65.945    480
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.43 %
    Favored  : 83.33 %
  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: -2.71 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 330 
 PHE   0.005   0.001   PHE G 346 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.002   0.000   ARG H 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6064 (mp0) cc_final: 0.5700 (mp0)
REVERT: C  369 LYS cc_start: 0.8548 (pttt) cc_final: 0.8315 (ptpt)
REVERT: F  311 LYS cc_start: 0.8521 (tptt) cc_final: 0.7891 (tppt)
REVERT: F  372 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8198 (mt-10)
REVERT: F  379 ARG cc_start: 0.7106 (ptp-170) cc_final: 0.6510 (ptm160)
REVERT: F  380 GLU cc_start: 0.6870 (tt0) cc_final: 0.5895 (pm20)
REVERT: D  349 ARG cc_start: 0.6644 (mtp180) cc_final: 0.5834 (mtt90)
REVERT: G  311 LYS cc_start: 0.8352 (tttt) cc_final: 0.7726 (tptp)
REVERT: G  319 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8109 (p)
REVERT: G  338 GLU cc_start: 0.6647 (mp0) cc_final: 0.5864 (mp0)
REVERT: G  340 LYS cc_start: 0.6211 (mmtm) cc_final: 0.5890 (tptp)
REVERT: E  317 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7702 (ptpp)
REVERT: E  368 ASN cc_start: 0.7962 (m-40) cc_final: 0.7672 (m-40)
REVERT: E  369 LYS cc_start: 0.8384 (pttt) cc_final: 0.8101 (ptpp)
REVERT: E  375 LYS cc_start: 0.8011 (tttt) cc_final: 0.7660 (mttm)
REVERT: H  328 ILE cc_start: 0.8176 (mt) cc_final: 0.7954 (mp)
REVERT: H  338 GLU cc_start: 0.6682 (mp0) cc_final: 0.6448 (mp0)
REVERT: H  369 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8006 (tttt)
REVERT: H  372 GLU cc_start: 0.8368 (tt0) cc_final: 0.8046 (mt-10)
  outliers start: 9
  outliers final: 8
  residues processed: 86
  average time/residue: 0.5541
  time to fit residues: 53.9857
Evaluate side-chains
  90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain D residue  317 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Chi-restraints excluded: chain H residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.174200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.140579 restraints weight = 12706.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.4308 rms_B_bonded: 2.43
r_work: 0.4237 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4136 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.5945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3582  Z= 0.184
  Angle     :  0.525   4.126   4794  Z= 0.266
  Chirality :  0.048   0.128    534
  Planarity :  0.003   0.038    618
  Dihedral  :  7.082  64.113    480
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.68 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 329 
 PHE   0.007   0.001   PHE G 346 
 TYR   0.013   0.002   TYR E 310 
 ARG   0.002   0.000   ARG H 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  338 GLU cc_start: 0.6055 (mp0) cc_final: 0.5670 (mp0)
REVERT: C  369 LYS cc_start: 0.8484 (pttt) cc_final: 0.8181 (ptpt)
REVERT: F  311 LYS cc_start: 0.8526 (tptt) cc_final: 0.7887 (tppt)
REVERT: F  372 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: F  379 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6520 (ptm160)
REVERT: F  380 GLU cc_start: 0.6831 (tt0) cc_final: 0.5816 (pm20)
REVERT: D  349 ARG cc_start: 0.6635 (mtp180) cc_final: 0.5825 (mtt90)
REVERT: G  311 LYS cc_start: 0.8355 (tttt) cc_final: 0.7720 (tptp)
REVERT: G  319 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (p)
REVERT: G  338 GLU cc_start: 0.6606 (mp0) cc_final: 0.5959 (mp0)
REVERT: G  372 GLU cc_start: 0.8558 (tt0) cc_final: 0.7921 (mt-10)
REVERT: E  317 LYS cc_start: 0.8384 (ptmt) cc_final: 0.7690 (ptpp)
REVERT: E  368 ASN cc_start: 0.7939 (m-40) cc_final: 0.7634 (m-40)
REVERT: E  369 LYS cc_start: 0.8397 (pttt) cc_final: 0.7795 (ptmm)
REVERT: E  375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7705 (mttm)
REVERT: H  328 ILE cc_start: 0.8154 (mt) cc_final: 0.7926 (mp)
REVERT: H  338 GLU cc_start: 0.6737 (mp0) cc_final: 0.6490 (mp0)
REVERT: H  369 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8027 (tttt)
REVERT: H  372 GLU cc_start: 0.8400 (tt0) cc_final: 0.8102 (mt-10)
  outliers start: 8
  outliers final: 7
  residues processed: 87
  average time/residue: 0.5571
  time to fit residues: 54.9692
Evaluate side-chains
  88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain D residue  317 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain H residue  358 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4655 r_free = 0.4655 target = 0.174375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.140786 restraints weight = 12653.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 2.49
r_work: 0.4251 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4150 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.6002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3582  Z= 0.178
  Angle     :  0.526   4.100   4794  Z= 0.267
  Chirality :  0.048   0.127    534
  Planarity :  0.003   0.038    618
  Dihedral  :  7.013  63.644    480
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.43 %
    Favored  : 83.83 %
  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: -2.70 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 329 
 PHE   0.007   0.001   PHE G 346 
 TYR   0.012   0.002   TYR E 310 
 ARG   0.002   0.000   ARG H 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5324.09 seconds
wall clock time: 97 minutes 28.31 seconds (5848.31 seconds total)