Starting phenix.real_space_refine
on Wed Sep 17 08:30:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bxr_45009/09_2025/9bxr_45009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bxr_45009/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bxr_45009/09_2025/9bxr_45009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bxr_45009/09_2025/9bxr_45009.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bxr_45009/09_2025/9bxr_45009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bxr_45009/09_2025/9bxr_45009.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.72, per 1000 atoms: 0.24
  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: 0.60
  Conformation dependent library (CDL) restraints added in 329.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.21
  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: 1.35

  Time building geometry restraints manager: 0.89 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:             1.590
  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:             0.050
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.600
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.000
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.860
-------------------------------------------------------------------------------
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= 0.718
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.61 (0.28), 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
 ARG   0.001   0.000   ARG H 379 
 TYR   0.057   0.021   TYR D 310 
 PHE   0.058   0.012   PHE F 346 
 HIS   0.010   0.003   HIS G 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01148 ( 3582)
  covalent geometry    : angle       1.86713 ( 4794)
  hydrogen bonds       : bond        0.18410 (   49)
  hydrogen bonds       : angle       7.35127 (  147)

*********************** 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  : 0.213 
Fit side-chains
   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: 0.6060 (mp0)
REVERT: C  369 LYS cc_start: 0.8214 (pttt) cc_final: 0.7943 (ptpt)
REVERT: F  337 VAL cc_start: 0.7330 (t) cc_final: 0.6933 (t)
REVERT: F  338 GLU cc_start: 0.6578 (mp0) cc_final: 0.6229 (mp0)
REVERT: F  379 ARG cc_start: 0.6781 (ptp-170) cc_final: 0.5723 (ptm160)
REVERT: D  353 LYS cc_start: 0.7642 (mttt) cc_final: 0.7143 (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: 0.6499 (t)
REVERT: G  338 GLU cc_start: 0.6400 (mp0) cc_final: 0.5503 (mp0)
REVERT: G  372 GLU cc_start: 0.8434 (tt0) cc_final: 0.8079 (mt-10)
REVERT: E  317 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7482 (ptpp)
REVERT: E  353 LYS cc_start: 0.7563 (mttt) cc_final: 0.7157 (mmtm)
REVERT: E  369 LYS cc_start: 0.8144 (pttt) cc_final: 0.7885 (ptpt)
REVERT: E  375 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8062 (mtpt)
REVERT: E  380 GLU cc_start: 0.5194 (tt0) cc_final: 0.4182 (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: 0.6298 (mp0)
REVERT: H  353 LYS cc_start: 0.7436 (mtpt) cc_final: 0.7179 (mttp)
REVERT: H  372 GLU cc_start: 0.8377 (tt0) cc_final: 0.7817 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2729
  time to fit residues: 31.7675
Evaluate side-chains
  77 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.4712 r_free = 0.4712 target = 0.182757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.147498 restraints weight = 12266.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.4363 rms_B_bonded: 2.47
r_work: 0.4295 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4196 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3582  Z= 0.145
  Angle     :  0.672   5.141   4794  Z= 0.358
  Chirality :  0.049   0.129    534
  Planarity :  0.003   0.019    618
  Dihedral  :  9.140  75.813    480
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  7.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.27), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.21), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 349 
 TYR   0.014   0.003   TYR D 310 
 PHE   0.016   0.003   PHE H 346 
 HIS   0.005   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3582)
  covalent geometry    : angle       0.67240 ( 4794)
  hydrogen bonds       : bond        0.03379 (   49)
  hydrogen bonds       : angle       5.31675 (  147)

*********************** 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
  99 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.203 
Fit side-chains
REVERT: C  338 GLU cc_start: 0.6171 (mp0) cc_final: 0.5799 (mp0)
REVERT: F  331 LYS cc_start: 0.8254 (mttm) cc_final: 0.7195 (mmtt)
REVERT: F  372 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: F  379 ARG cc_start: 0.7187 (ptp-170) cc_final: 0.6475 (ptm160)
REVERT: F  380 GLU cc_start: 0.7192 (tt0) cc_final: 0.5874 (pm20)
REVERT: D  314 ASP cc_start: 0.7659 (m-30) cc_final: 0.7419 (t70)
REVERT: D  353 LYS cc_start: 0.7786 (mttt) cc_final: 0.7464 (tppt)
REVERT: D  379 ARG cc_start: 0.7638 (mpt180) cc_final: 0.7354 (mpt180)
REVERT: G  311 LYS cc_start: 0.8460 (mttt) cc_final: 0.8195 (tmtt)
REVERT: G  336 GLN cc_start: 0.7041 (mt0) cc_final: 0.5963 (mp-120)
REVERT: G  337 VAL cc_start: 0.7304 (t) cc_final: 0.6561 (t)
REVERT: G  338 GLU cc_start: 0.6601 (mp0) cc_final: 0.5905 (mp0)
REVERT: G  372 GLU cc_start: 0.8407 (tt0) cc_final: 0.8008 (mt-10)
REVERT: E  314 ASP cc_start: 0.7753 (m-30) cc_final: 0.7390 (t0)
REVERT: E  317 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7758 (ptpp)
REVERT: E  368 ASN cc_start: 0.7983 (m-40) cc_final: 0.7645 (m-40)
REVERT: E  369 LYS cc_start: 0.8282 (pttt) cc_final: 0.8079 (ptpt)
REVERT: E  375 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7942 (mttm)
REVERT: H  337 VAL cc_start: 0.6642 (t) cc_final: 0.6371 (t)
REVERT: H  338 GLU cc_start: 0.6460 (mp0) cc_final: 0.6187 (mp0)
REVERT: H  351 GLN cc_start: 0.6608 (pt0) cc_final: 0.5555 (pm20)
REVERT: H  369 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8048 (tttt)
REVERT: H  372 GLU cc_start: 0.8209 (tt0) cc_final: 0.7820 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 97
  average time/residue: 0.2170
  time to fit residues: 24.2095
Evaluate side-chains
  79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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 36 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 359 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.181370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.146364 restraints weight = 12228.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.4377 rms_B_bonded: 2.44
r_work: 0.4310 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.4210 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3582  Z= 0.097
  Angle     :  0.553   3.722   4794  Z= 0.286
  Chirality :  0.049   0.130    534
  Planarity :  0.002   0.018    618
  Dihedral  :  8.015  67.764    480
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  8.71 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.28), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.011   0.002   TYR D 310 
 PHE   0.010   0.002   PHE H 346 
 HIS   0.002   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3582)
  covalent geometry    : angle       0.55250 ( 4794)
  hydrogen bonds       : bond        0.02676 (   49)
  hydrogen bonds       : angle       4.54740 (  147)

*********************** 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: 10
    poor density    : 83
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  331 LYS cc_start: 0.7269 (ttmt) cc_final: 0.6955 (tttt)
REVERT: C  338 GLU cc_start: 0.6206 (mp0) cc_final: 0.5852 (mp0)
REVERT: F  311 LYS cc_start: 0.8515 (tptt) cc_final: 0.8025 (tptm)
REVERT: F  331 LYS cc_start: 0.8290 (mttm) cc_final: 0.7174 (mmtt)
REVERT: F  372 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: F  379 ARG cc_start: 0.7138 (ptp-170) cc_final: 0.6438 (ptm160)
REVERT: F  380 GLU cc_start: 0.6929 (tt0) cc_final: 0.5875 (pm20)
REVERT: D  349 ARG cc_start: 0.6796 (mtp180) cc_final: 0.5928 (mtt90)
REVERT: D  353 LYS cc_start: 0.7836 (mttt) cc_final: 0.7516 (tppt)
REVERT: G  311 LYS cc_start: 0.8504 (mttt) cc_final: 0.8274 (tttt)
REVERT: G  337 VAL cc_start: 0.7382 (t) cc_final: 0.6793 (t)
REVERT: G  338 GLU cc_start: 0.6713 (mp0) cc_final: 0.6073 (mp0)
REVERT: G  372 GLU cc_start: 0.8381 (tt0) cc_final: 0.8064 (mt-10)
REVERT: E  317 LYS cc_start: 0.8386 (ptmt) cc_final: 0.7820 (ptpp)
REVERT: E  353 LYS cc_start: 0.7936 (tttm) cc_final: 0.7735 (tppt)
REVERT: E  368 ASN cc_start: 0.7997 (m-40) cc_final: 0.7660 (m-40)
REVERT: E  369 LYS cc_start: 0.8298 (pttt) cc_final: 0.8031 (ptpp)
REVERT: E  375 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7964 (mttm)
REVERT: H  311 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8352 (mttt)
REVERT: H  328 ILE cc_start: 0.8148 (mt) cc_final: 0.7845 (mp)
REVERT: H  338 GLU cc_start: 0.6542 (mp0) cc_final: 0.6306 (mp0)
REVERT: H  351 GLN cc_start: 0.6446 (pt0) cc_final: 0.5319 (pm20)
REVERT: H  372 GLU cc_start: 0.8250 (tt0) cc_final: 0.7859 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 89
  average time/residue: 0.2432
  time to fit residues: 24.5509
Evaluate side-chains
  85 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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 G residue  359 ASN
Chi-restraints excluded: chain G residue  376 LEU
Chi-restraints excluded: chain H residue  358 ASP
Chi-restraints excluded: chain H residue  359 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.3786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.179040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.144725 restraints weight = 12360.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.4372 rms_B_bonded: 2.39
r_work: 0.4304 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.4204 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4788

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= 0.117
  Angle     :  0.552   4.049   4794  Z= 0.283
  Chirality :  0.049   0.126    534
  Planarity :  0.003   0.024    618
  Dihedral  :  7.834  67.336    480
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.45 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.013   0.002   TYR D 310 
 PHE   0.009   0.002   PHE H 346 
 HIS   0.003   0.001   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3582)
  covalent geometry    : angle       0.55175 ( 4794)
  hydrogen bonds       : bond        0.02504 (   49)
  hydrogen bonds       : angle       4.46548 (  147)

*********************** 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
  84 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 LYS cc_start: 0.7268 (ttmt) cc_final: 0.7009 (tttt)
REVERT: C  338 GLU cc_start: 0.6345 (mp0) cc_final: 0.5974 (mp0)
REVERT: F  311 LYS cc_start: 0.8526 (tptt) cc_final: 0.8048 (tptm)
REVERT: F  372 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: F  379 ARG cc_start: 0.7139 (ptp-170) cc_final: 0.6495 (ptm160)
REVERT: F  380 GLU cc_start: 0.7036 (tt0) cc_final: 0.5995 (pm20)
REVERT: D  349 ARG cc_start: 0.6834 (mtp180) cc_final: 0.5984 (mtt90)
REVERT: G  311 LYS cc_start: 0.8529 (mttt) cc_final: 0.8297 (tttt)
REVERT: G  337 VAL cc_start: 0.7395 (t) cc_final: 0.6882 (t)
REVERT: G  338 GLU cc_start: 0.6792 (mp0) cc_final: 0.6206 (mp0)
REVERT: G  372 GLU cc_start: 0.8366 (tt0) cc_final: 0.8118 (mt-10)
REVERT: E  317 LYS cc_start: 0.8390 (ptmt) cc_final: 0.7839 (ptpp)
REVERT: E  327 ASN cc_start: 0.8414 (p0) cc_final: 0.8204 (p0)
REVERT: E  368 ASN cc_start: 0.8034 (m-40) cc_final: 0.7710 (m-40)
REVERT: E  369 LYS cc_start: 0.8339 (pttt) cc_final: 0.8074 (ptpp)
REVERT: E  375 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7989 (mttm)
REVERT: H  328 ILE cc_start: 0.8184 (mt) cc_final: 0.7913 (mp)
REVERT: H  338 GLU cc_start: 0.6601 (mp0) cc_final: 0.6369 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 81
  average time/residue: 0.2601
  time to fit residues: 23.8190
Evaluate side-chains
  79 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain H residue  361 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
G 359 ASN
H 359 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.180690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.146130 restraints weight = 12280.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.4370 rms_B_bonded: 2.46
r_work: 0.4298 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4196 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3582  Z= 0.089
  Angle     :  0.501   3.655   4794  Z= 0.254
  Chirality :  0.048   0.129    534
  Planarity :  0.002   0.026    618
  Dihedral  :  7.529  68.558    480
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.010   0.002   TYR E 310 
 PHE   0.007   0.001   PHE H 346 
 HIS   0.003   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 3582)
  covalent geometry    : angle       0.50145 ( 4794)
  hydrogen bonds       : bond        0.02075 (   49)
  hydrogen bonds       : angle       4.24127 (  147)

*********************** 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
  94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 LYS cc_start: 0.7270 (ttmt) cc_final: 0.7000 (tttt)
REVERT: C  338 GLU cc_start: 0.6125 (mp0) cc_final: 0.5760 (mp0)
REVERT: F  311 LYS cc_start: 0.8513 (tptt) cc_final: 0.7898 (tppt)
REVERT: F  372 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8122 (mt-10)
REVERT: F  379 ARG cc_start: 0.7216 (ptp-170) cc_final: 0.6454 (ptm160)
REVERT: F  380 GLU cc_start: 0.6974 (tt0) cc_final: 0.5884 (pm20)
REVERT: D  349 ARG cc_start: 0.6728 (mtp180) cc_final: 0.5869 (mtt90)
REVERT: G  311 LYS cc_start: 0.8506 (mttt) cc_final: 0.8225 (tttt)
REVERT: G  337 VAL cc_start: 0.7358 (t) cc_final: 0.6842 (t)
REVERT: G  338 GLU cc_start: 0.6706 (mp0) cc_final: 0.6026 (mp0)
REVERT: G  372 GLU cc_start: 0.8472 (tt0) cc_final: 0.8196 (mt-10)
REVERT: E  317 LYS cc_start: 0.8385 (ptmt) cc_final: 0.7756 (ptpp)
REVERT: E  353 LYS cc_start: 0.8119 (tttm) cc_final: 0.7842 (tppt)
REVERT: E  368 ASN cc_start: 0.8010 (m-40) cc_final: 0.7666 (m-40)
REVERT: E  369 LYS cc_start: 0.8370 (pttt) cc_final: 0.8095 (ptpp)
REVERT: E  375 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7930 (mttm)
REVERT: H  328 ILE cc_start: 0.8105 (mt) cc_final: 0.7824 (mp)
REVERT: H  338 GLU cc_start: 0.6706 (mp0) cc_final: 0.6506 (mp0)
REVERT: H  372 GLU cc_start: 0.8294 (tt0) cc_final: 0.7913 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 90
  average time/residue: 0.2437
  time to fit residues: 24.9405
Evaluate side-chains
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 G residue  359 ASN
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 34 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.0984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.178812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.144836 restraints weight = 12489.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.4368 rms_B_bonded: 2.53
r_work: 0.4293 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.4190 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3582  Z= 0.098
  Angle     :  0.509   3.693   4794  Z= 0.258
  Chirality :  0.048   0.125    534
  Planarity :  0.003   0.030    618
  Dihedral  :  7.371  67.582    480
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.011   0.002   TYR E 310 
 PHE   0.006   0.001   PHE G 346 
 HIS   0.003   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 3582)
  covalent geometry    : angle       0.50904 ( 4794)
  hydrogen bonds       : bond        0.02054 (   49)
  hydrogen bonds       : angle       4.24392 (  147)

*********************** 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
  94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6945 (tttt)
REVERT: C  338 GLU cc_start: 0.6100 (mp0) cc_final: 0.5760 (mp0)
REVERT: F  311 LYS cc_start: 0.8499 (tptt) cc_final: 0.7862 (tppt)
REVERT: F  372 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: F  379 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6395 (ptm160)
REVERT: F  380 GLU cc_start: 0.6951 (tt0) cc_final: 0.5823 (pm20)
REVERT: G  311 LYS cc_start: 0.8514 (mttt) cc_final: 0.8190 (tttt)
REVERT: G  337 VAL cc_start: 0.7305 (t) cc_final: 0.6823 (t)
REVERT: G  338 GLU cc_start: 0.6711 (mp0) cc_final: 0.6104 (mp0)
REVERT: G  372 GLU cc_start: 0.8478 (tt0) cc_final: 0.8203 (mt-10)
REVERT: E  317 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7706 (ptpp)
REVERT: E  327 ASN cc_start: 0.8330 (p0) cc_final: 0.8128 (p0)
REVERT: E  368 ASN cc_start: 0.7987 (m-40) cc_final: 0.7632 (m-40)
REVERT: E  369 LYS cc_start: 0.8343 (pttt) cc_final: 0.8038 (ptpp)
REVERT: H  328 ILE cc_start: 0.8046 (mt) cc_final: 0.7756 (mp)
REVERT: H  372 GLU cc_start: 0.8350 (tt0) cc_final: 0.7930 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 90
  average time/residue: 0.2548
  time to fit residues: 25.9900
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  : 0.201 
-------------------------------------------------------------------------------
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  361 THR
Chi-restraints excluded: chain H residue  358 ASP
Chi-restraints excluded: chain H residue  359 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** H 330 HIS ** 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 = 0.4698 r_free = 0.4698 target = 0.176898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.143374 restraints weight = 12520.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4359 rms_B_bonded: 2.44
r_work: 0.4287 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4185 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.5473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3582  Z= 0.101
  Angle     :  0.511   3.721   4794  Z= 0.258
  Chirality :  0.048   0.127    534
  Planarity :  0.003   0.034    618
  Dihedral  :  7.177  66.039    480
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.18 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.31), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.012   0.002   TYR E 310 
 PHE   0.007   0.001   PHE G 346 
 HIS   0.003   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 3582)
  covalent geometry    : angle       0.51103 ( 4794)
  hydrogen bonds       : bond        0.02172 (   49)
  hydrogen bonds       : angle       4.19783 (  147)

*********************** 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
  92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 LYS cc_start: 0.7298 (ttmt) cc_final: 0.7014 (tttt)
REVERT: C  338 GLU cc_start: 0.6148 (mp0) cc_final: 0.5807 (mp0)
REVERT: F  311 LYS cc_start: 0.8496 (tptt) cc_final: 0.7878 (tppt)
REVERT: F  372 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: F  380 GLU cc_start: 0.6919 (tt0) cc_final: 0.5943 (pm20)
REVERT: G  311 LYS cc_start: 0.8502 (mttt) cc_final: 0.8237 (tttt)
REVERT: G  338 GLU cc_start: 0.6460 (mp0) cc_final: 0.6250 (mp0)
REVERT: E  317 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7712 (ptpp)
REVERT: E  327 ASN cc_start: 0.8404 (p0) cc_final: 0.8165 (p0)
REVERT: E  368 ASN cc_start: 0.8012 (m-40) cc_final: 0.7680 (m-40)
REVERT: E  369 LYS cc_start: 0.8331 (pttt) cc_final: 0.8038 (ptpp)
REVERT: H  328 ILE cc_start: 0.8108 (mt) cc_final: 0.7824 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 89
  average time/residue: 0.2295
  time to fit residues: 23.5215
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  : 0.218 
-------------------------------------------------------------------------------
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 D residue  369 LYS
Chi-restraints excluded: chain H residue  358 ASP
Chi-restraints excluded: chain H residue  359 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 6 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** H 330 HIS ** 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 = 0.4728 r_free = 0.4728 target = 0.179876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.146191 restraints weight = 12444.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.4401 rms_B_bonded: 2.53
r_work: 0.4327 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4225 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3582  Z= 0.078
  Angle     :  0.478   3.645   4794  Z= 0.241
  Chirality :  0.048   0.125    534
  Planarity :  0.003   0.033    618
  Dihedral  :  7.031  65.884    480
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.18 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.009   0.002   TYR E 310 
 PHE   0.005   0.001   PHE G 346 
 HIS   0.003   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 3582)
  covalent geometry    : angle       0.47838 ( 4794)
  hydrogen bonds       : bond        0.02008 (   49)
  hydrogen bonds       : angle       4.02819 (  147)

*********************** 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
  93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6949 (tttt)
REVERT: C  338 GLU cc_start: 0.6034 (mp0) cc_final: 0.5357 (mp0)
REVERT: F  311 LYS cc_start: 0.8484 (tptt) cc_final: 0.7840 (tppt)
REVERT: F  372 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: F  380 GLU cc_start: 0.6903 (tt0) cc_final: 0.6145 (mm-30)
REVERT: G  311 LYS cc_start: 0.8471 (mttt) cc_final: 0.8188 (tttt)
REVERT: G  338 GLU cc_start: 0.6563 (mp0) cc_final: 0.5985 (mp0)
REVERT: G  359 ASN cc_start: 0.5693 (t0) cc_final: 0.5309 (t0)
REVERT: G  372 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8111 (mm-30)
REVERT: E  317 LYS cc_start: 0.8387 (ptmt) cc_final: 0.7703 (ptpp)
REVERT: E  368 ASN cc_start: 0.8052 (m-40) cc_final: 0.7737 (m-40)
REVERT: E  369 LYS cc_start: 0.8346 (pttt) cc_final: 0.8034 (ptpp)
REVERT: H  328 ILE cc_start: 0.8060 (mt) cc_final: 0.7755 (mp)
REVERT: H  338 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6553 (mm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 90
  average time/residue: 0.2301
  time to fit residues: 23.7774
Evaluate side-chains
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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 H residue  358 ASP
Chi-restraints excluded: chain H residue  359 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** H 330 HIS ** 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 = 0.4698 r_free = 0.4698 target = 0.176851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.143343 restraints weight = 12495.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.4344 rms_B_bonded: 2.49
r_work: 0.4269 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4166 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3582  Z= 0.109
  Angle     :  0.516   3.907   4794  Z= 0.261
  Chirality :  0.048   0.127    534
  Planarity :  0.003   0.036    618
  Dihedral  :  6.966  63.282    480
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.93 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.012   0.002   TYR E 310 
 PHE   0.008   0.001   PHE G 346 
 HIS   0.004   0.001   HIS F 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3582)
  covalent geometry    : angle       0.51591 ( 4794)
  hydrogen bonds       : bond        0.02071 (   49)
  hydrogen bonds       : angle       4.12570 (  147)

*********************** 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
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.207 
Fit side-chains
REVERT: C  331 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6937 (tttt)
REVERT: C  338 GLU cc_start: 0.5996 (mp0) cc_final: 0.5638 (mp0)
REVERT: F  311 LYS cc_start: 0.8485 (tptt) cc_final: 0.7848 (tppt)
REVERT: F  372 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: F  380 GLU cc_start: 0.6816 (tt0) cc_final: 0.6077 (mm-30)
REVERT: G  311 LYS cc_start: 0.8448 (mttt) cc_final: 0.8168 (tttt)
REVERT: G  337 VAL cc_start: 0.7147 (t) cc_final: 0.6728 (t)
REVERT: G  338 GLU cc_start: 0.6525 (mp0) cc_final: 0.5962 (mp0)
REVERT: G  372 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8289 (mt-10)
REVERT: E  317 LYS cc_start: 0.8375 (ptmt) cc_final: 0.7679 (ptpp)
REVERT: E  342 GLU cc_start: 0.3304 (pm20) cc_final: 0.2183 (pm20)
REVERT: E  353 LYS cc_start: 0.8214 (tttm) cc_final: 0.7875 (tppt)
REVERT: E  368 ASN cc_start: 0.7971 (m-40) cc_final: 0.7622 (m-40)
REVERT: E  369 LYS cc_start: 0.8360 (pttt) cc_final: 0.8037 (ptpp)
REVERT: H  328 ILE cc_start: 0.8009 (mt) cc_final: 0.7732 (mp)
REVERT: H  338 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6391 (mm-30)
REVERT: H  369 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7977 (tttt)
REVERT: H  372 GLU cc_start: 0.8360 (tt0) cc_final: 0.8043 (mt-10)
  outliers start: 6
  outliers final: 5
  residues processed: 83
  average time/residue: 0.2343
  time to fit residues: 22.3997
Evaluate side-chains
  85 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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 H residue  358 ASP
Chi-restraints excluded: chain H residue  359 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** H 330 HIS ** 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 = 0.4702 r_free = 0.4702 target = 0.177405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.144115 restraints weight = 12446.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4362 rms_B_bonded: 2.47
r_work: 0.4287 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4185 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.5818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3582  Z= 0.095
  Angle     :  0.499   4.076   4794  Z= 0.251
  Chirality :  0.048   0.125    534
  Planarity :  0.003   0.037    618
  Dihedral  :  6.908  63.941    480
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.43 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.24), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 379 
 TYR   0.011   0.002   TYR D 310 
 PHE   0.006   0.001   PHE H 346 
 HIS   0.003   0.001   HIS F 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3582)
  covalent geometry    : angle       0.49934 ( 4794)
  hydrogen bonds       : bond        0.01997 (   49)
  hydrogen bonds       : angle       4.09003 (  147)

********************** 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
  88 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.205 
Fit side-chains
REVERT: C  331 LYS cc_start: 0.7203 (ttmt) cc_final: 0.6921 (tttt)
REVERT: C  338 GLU cc_start: 0.5998 (mp0) cc_final: 0.5625 (mp0)
REVERT: F  311 LYS cc_start: 0.8475 (tptt) cc_final: 0.7839 (tppt)
REVERT: F  340 LYS cc_start: 0.6354 (tmtt) cc_final: 0.5759 (ttmm)
REVERT: F  372 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8162 (mt-10)
REVERT: F  379 ARG cc_start: 0.7127 (ptp-170) cc_final: 0.6599 (ptm160)
REVERT: F  380 GLU cc_start: 0.6810 (tt0) cc_final: 0.5810 (pm20)
REVERT: G  311 LYS cc_start: 0.8450 (mttt) cc_final: 0.8163 (tttt)
REVERT: G  337 VAL cc_start: 0.7166 (t) cc_final: 0.6754 (t)
REVERT: G  338 GLU cc_start: 0.6563 (mp0) cc_final: 0.6016 (mp0)
REVERT: G  372 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8327 (mt-10)
REVERT: E  317 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7697 (ptpp)
REVERT: E  342 GLU cc_start: 0.3436 (pm20) cc_final: 0.2264 (pm20)
REVERT: E  353 LYS cc_start: 0.8247 (tttm) cc_final: 0.7856 (tppt)
REVERT: E  368 ASN cc_start: 0.7982 (m-40) cc_final: 0.7655 (m-40)
REVERT: E  369 LYS cc_start: 0.8388 (pttt) cc_final: 0.8069 (ptpp)
REVERT: H  328 ILE cc_start: 0.8020 (mt) cc_final: 0.7735 (mp)
REVERT: H  338 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6426 (mm-30)
REVERT: H  372 GLU cc_start: 0.8360 (tt0) cc_final: 0.8036 (mt-10)
  outliers start: 6
  outliers final: 5
  residues processed: 85
  average time/residue: 0.2317
  time to fit residues: 22.5110
Evaluate side-chains
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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 H residue  358 ASP
Chi-restraints excluded: chain H residue  359 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.178546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.145137 restraints weight = 12454.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 2.48
r_work: 0.4300 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.4197 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3582  Z= 0.085
  Angle     :  0.483   4.067   4794  Z= 0.242
  Chirality :  0.048   0.126    534
  Planarity :  0.003   0.037    618
  Dihedral  :  6.736  63.203    480
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.32), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.25), residues: 450

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 3582)
  covalent geometry    : angle       0.48273 ( 4794)
  hydrogen bonds       : bond        0.01886 (   49)
  hydrogen bonds       : angle       4.01958 (  147)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2826.68 seconds
wall clock time: 48 minutes 43.58 seconds (2923.58 seconds total)