Starting phenix.real_space_refine
on Wed Sep 17 03:57:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hrf_0260/09_2025/6hrf_0260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hrf_0260/09_2025/6hrf_0260.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hrf_0260/09_2025/6hrf_0260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hrf_0260/09_2025/6hrf_0260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hrf_0260/09_2025/6hrf_0260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hrf_0260/09_2025/6hrf_0260.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2202      2.51       5
     N     648      2.21       5
     O     666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 3522
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.80, per 1000 atoms: 0.23
  Number of scatterers: 3522
  At special positions: 0
  Unit cell: (115.44, 118.56, 37.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     666      8.00
     N     648      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 132.8 milliseconds
  
  Enol-peptide restraints added in 238.4 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 18 sheets defined
      0.0% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.632A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL C 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 'A' and resid 318 through 322
      removed outlier: 7.197A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   THR C 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   CYS E 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330
      removed outlier: 6.810A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   HIS C 329 " --> pdb=" O   HIS E 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 341
    Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 353
      removed outlier: 6.691A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLN C 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359
      removed outlier: 7.330A  pdb=" N   SER A 356 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   ASN C 359 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   SER C 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ASN E 359 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ASP C 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 371
    Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.549A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   PHE E 378 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   THR C 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310
    Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.558A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL D 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322
      removed outlier: 7.138A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   THR D 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   CYS F 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LYS D 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 330
      removed outlier: 6.873A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   HIS D 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 339 through 341
      removed outlier: 3.550A  pdb=" N   LYS B 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER D 341 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER F 341 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 351 through 353
      removed outlier: 6.764A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   GLN D 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 356 through 359
      removed outlier: 7.381A  pdb=" N   SER B 356 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   ASN D 359 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   SER D 356 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   ASN F 359 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASP D 358 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 369 through 371
    Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 378
      removed outlier: 6.610A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LYS D 375 " --> pdb=" O   LEU F 376 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   PHE F 378 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   THR D 377 " --> pdb=" O   PHE F 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    33 hydrogen bonds defined for protein.
    99 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: 0.44

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 630
        1.32 -     1.44: 788
        1.44 -     1.55: 2027
        1.55 -     1.67: 125
        1.67 -     1.79: 6
  Bond restraints: 3576
  Sorted by residual:
  bond pdb=" C   LYS E 311 "
       pdb=" N   PRO E 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.386 -0.053 1.17e-02 7.31e+03 2.07e+01
  bond pdb=" C   LYS B 311 "
       pdb=" N   PRO B 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.386 -0.053 1.17e-02 7.31e+03 2.04e+01
  bond pdb=" C   LYS C 311 "
       pdb=" N   PRO C 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.385 -0.053 1.17e-02 7.31e+03 2.03e+01
  bond pdb=" N   ARG B 349 "
       pdb=" CA  ARG B 349 "
    ideal  model  delta    sigma   weight residual
    1.457  1.529 -0.071 1.58e-02 4.01e+03 2.03e+01
  bond pdb=" C   LYS A 311 "
       pdb=" N   PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.385 -0.053 1.17e-02 7.31e+03 2.02e+01
  ... (remaining 3571 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 4011
        1.38 -     2.76: 519
        2.76 -     4.14: 163
        4.14 -     5.51: 71
        5.51 -     6.89: 18
  Bond angle restraints: 4782
  Sorted by residual:
  angle pdb=" N   SER F 352 "
        pdb=" CA  SER F 352 "
        pdb=" C   SER F 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER A 352 "
        pdb=" CA  SER A 352 "
        pdb=" C   SER A 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER E 352 "
        pdb=" CA  SER E 352 "
        pdb=" C   SER E 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER C 352 "
        pdb=" CA  SER C 352 "
        pdb=" C   SER C 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER D 352 "
        pdb=" CA  SER D 352 "
        pdb=" C   SER D 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.68   -5.69 1.57e+00 4.06e-01 1.31e+01
  ... (remaining 4777 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.36: 1896
       13.36 -    26.71: 174
       26.71 -    40.06: 72
       40.06 -    53.41: 24
       53.41 -    66.76: 12
  Dihedral angle restraints: 2178
    sinusoidal: 912
      harmonic: 1266
  Sorted by residual:
  dihedral pdb=" CB  LYS B 353 "
           pdb=" CG  LYS B 353 "
           pdb=" CD  LYS B 353 "
           pdb=" CE  LYS B 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.76   41.76     3      1.50e+01 4.44e-03 7.48e+00
  dihedral pdb=" CB  LYS A 353 "
           pdb=" CG  LYS A 353 "
           pdb=" CD  LYS A 353 "
           pdb=" CE  LYS A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.73   41.73     3      1.50e+01 4.44e-03 7.47e+00
  dihedral pdb=" CB  LYS D 353 "
           pdb=" CG  LYS D 353 "
           pdb=" CD  LYS D 353 "
           pdb=" CE  LYS D 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.72   41.72     3      1.50e+01 4.44e-03 7.47e+00
  ... (remaining 2175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 227
       0.050 -    0.099: 142
       0.099 -    0.149: 81
       0.149 -    0.198: 72
       0.198 -    0.248: 12
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  ILE D 328 "
            pdb=" N   ILE D 328 "
            pdb=" C   ILE D 328 "
            pdb=" CB  ILE D 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  ILE B 328 "
            pdb=" N   ILE B 328 "
            pdb=" C   ILE B 328 "
            pdb=" CB  ILE B 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  ILE C 328 "
            pdb=" N   ILE C 328 "
            pdb=" C   ILE C 328 "
            pdb=" CB  ILE C 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 531 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E 368 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   ASN E 368 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN E 368 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS E 369 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 368 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   ASN A 368 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN A 368 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS A 369 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 368 "   -0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   ASN B 368 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASN B 368 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS B 369 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 2011
        3.08 -     3.54: 3350
        3.54 -     3.99: 5016
        3.99 -     4.45: 4850
        4.45 -     4.90: 9434
  Nonbonded interactions: 24661
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 316 "
            pdb=" NZ  LYS B 370 "
     model   vdw
     2.627 3.120
  nonbonded pdb=" OG  SER D 316 "
            pdb=" NZ  LYS D 370 "
     model   vdw
     2.628 3.120
  nonbonded pdb=" OG  SER A 316 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.628 3.120
  nonbonded pdb=" OG  SER C 316 "
            pdb=" NZ  LYS C 370 "
     model   vdw
     2.628 3.120
  nonbonded pdb=" OG  SER E 316 "
            pdb=" NZ  LYS E 370 "
     model   vdw
     2.628 3.120
  ... (remaining 24656 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.230
  Find NCS groups from input model:        0.030
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
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      :  0.016   0.071   3576  Z= 1.075
  Angle     :  1.247   6.892   4782  Z= 0.750
  Chirality :  0.093   0.248    534
  Planarity :  0.010   0.038    612
  Dihedral  : 13.679  66.761   1374
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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: -4.08 (0.28), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.21), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.003   ARG B 349 
 TYR   0.033   0.014   TYR C 310 
 PHE   0.027   0.008   PHE C 346 
 HIS   0.009   0.003   HIS E 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01591 ( 3576)
  covalent geometry    : angle       1.24686 ( 4782)
  hydrogen bonds       : bond        0.21344 (   33)
  hydrogen bonds       : angle       7.35327 (   99)

*********************** 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
  147 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8535 (mtmt) cc_final: 0.7769 (mmmt)
REVERT: A  317 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8154 (ptpp)
REVERT: A  349 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7108 (mtm180)
REVERT: A  353 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7648 (tttm)
REVERT: B  311 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8307 (mmmt)
REVERT: C  317 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7508 (ptpp)
REVERT: C  343 LYS cc_start: 0.8134 (mttp) cc_final: 0.7818 (ttmm)
REVERT: C  349 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7740 (mtm-85)
REVERT: D  327 ASN cc_start: 0.7756 (p0) cc_final: 0.7370 (p0)
REVERT: E  317 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7763 (ptpp)
REVERT: E  349 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7920 (mtm180)
REVERT: E  361 THR cc_start: 0.9083 (m) cc_final: 0.8878 (t)
REVERT: E  379 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6404 (ptt-90)
REVERT: F  310 TYR cc_start: 0.8833 (t80) cc_final: 0.8616 (t80)
REVERT: F  311 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8439 (mtpt)
REVERT: F  327 ASN cc_start: 0.8104 (p0) cc_final: 0.7629 (p0)
REVERT: F  379 ARG cc_start: 0.6578 (mtt180) cc_final: 0.5019 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1521
  time to fit residues: 24.5717
Evaluate side-chains
  87 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 336 GLN
** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 336 GLN
F 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.150256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.124375 restraints weight = 5463.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 3.19
r_work: 0.3890 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3576  Z= 0.177
  Angle     :  0.643   6.223   4782  Z= 0.327
  Chirality :  0.049   0.142    534
  Planarity :  0.004   0.028    612
  Dihedral  :  4.968  12.227    474
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.20 %
    Favored  : 87.81 %
  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: -3.73 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 379 
 TYR   0.015   0.002   TYR D 310 
 PHE   0.007   0.002   PHE C 346 
 HIS   0.011   0.002   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3576)
  covalent geometry    : angle       0.64337 ( 4782)
  hydrogen bonds       : bond        0.02730 (   33)
  hydrogen bonds       : angle       6.15173 (   99)

*********************** 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
  109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8671 (mtmt) cc_final: 0.7983 (mmtm)
REVERT: A  317 LYS cc_start: 0.8569 (ptpt) cc_final: 0.7899 (ptpp)
REVERT: A  349 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7433 (mtm180)
REVERT: A  353 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7339 (tppt)
REVERT: B  311 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8333 (mmtt)
REVERT: C  338 GLU cc_start: 0.7617 (mp0) cc_final: 0.7017 (tm-30)
REVERT: C  349 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.7151 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8068 (p0) cc_final: 0.7552 (p0)
REVERT: E  342 GLU cc_start: 0.3177 (pm20) cc_final: 0.2603 (pm20)
REVERT: E  343 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7156 (mtmm)
REVERT: E  379 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6603 (ptt-90)
REVERT: F  311 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8686 (mtpt)
REVERT: F  327 ASN cc_start: 0.8351 (p0) cc_final: 0.8015 (p0)
REVERT: F  379 ARG cc_start: 0.6496 (mtt180) cc_final: 0.5790 (mtm180)
  outliers start: 8
  outliers final: 6
  residues processed: 104
  average time/residue: 0.1268
  time to fit residues: 14.8369
Evaluate side-chains
  102 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  377 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.0870
   chunk 28 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0030
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.1772

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
C 329 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.153011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.127123 restraints weight = 5339.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 3.19
r_work: 0.3917 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3576  Z= 0.105
  Angle     :  0.586   6.694   4782  Z= 0.282
  Chirality :  0.047   0.123    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.341  13.173    474
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.68 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.58 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 379 
 TYR   0.017   0.002   TYR D 310 
 PHE   0.008   0.001   PHE F 346 
 HIS   0.006   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3576)
  covalent geometry    : angle       0.58597 ( 4782)
  hydrogen bonds       : bond        0.01758 (   33)
  hydrogen bonds       : angle       5.82079 (   99)

*********************** 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
  108 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8633 (mtmt) cc_final: 0.7936 (mmtm)
REVERT: A  317 LYS cc_start: 0.8556 (ptpt) cc_final: 0.7883 (ptpp)
REVERT: A  336 GLN cc_start: 0.7588 (mp10) cc_final: 0.7170 (tm-30)
REVERT: A  338 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6687 (tm-30)
REVERT: A  349 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7600 (mtm180)
REVERT: A  353 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7553 (tttm)
REVERT: B  311 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8333 (mmtt)
REVERT: B  336 GLN cc_start: 0.7566 (pp30) cc_final: 0.6721 (pp30)
REVERT: B  351 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: C  338 GLU cc_start: 0.7790 (mp0) cc_final: 0.7079 (tm-30)
REVERT: C  349 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7343 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8123 (p0) cc_final: 0.7650 (p0)
REVERT: E  342 GLU cc_start: 0.3487 (pm20) cc_final: 0.2806 (pm20)
REVERT: E  343 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6991 (mtmm)
REVERT: E  372 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8039 (mm-30)
REVERT: E  379 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6602 (ptt-90)
REVERT: F  311 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8642 (mtpt)
REVERT: F  375 LYS cc_start: 0.8769 (tttt) cc_final: 0.8557 (ttmt)
REVERT: F  379 ARG cc_start: 0.6662 (mtt180) cc_final: 0.5885 (mtm180)
  outliers start: 8
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1178
  time to fit residues: 13.7797
Evaluate side-chains
  103 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 4 optimal weight:    7.9990
   chunk 11 optimal weight:   30.0000
   chunk 3 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    5.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.145963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.122313 restraints weight = 5588.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 3.14
r_work: 0.3802 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.5918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3576  Z= 0.285
  Angle     :  0.731   6.530   4782  Z= 0.364
  Chirality :  0.049   0.140    534
  Planarity :  0.004   0.025    612
  Dihedral  :  5.433  16.067    474
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.17 %
    Favored  : 80.85 %
  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: -3.66 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 379 
 TYR   0.011   0.002   TYR A 310 
 PHE   0.018   0.002   PHE B 378 
 HIS   0.008   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 3576)
  covalent geometry    : angle       0.73126 ( 4782)
  hydrogen bonds       : bond        0.02816 (   33)
  hydrogen bonds       : angle       5.59711 (   99)

*********************** 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
  128 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8067 (mmtm)
REVERT: A  317 LYS cc_start: 0.8631 (ptpt) cc_final: 0.7980 (ptpp)
REVERT: A  336 GLN cc_start: 0.7464 (mp10) cc_final: 0.7130 (tm-30)
REVERT: A  338 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6684 (tm-30)
REVERT: A  349 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7420 (mtm180)
REVERT: B  311 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8321 (mmtt)
REVERT: B  327 ASN cc_start: 0.8040 (p0) cc_final: 0.7830 (p0)
REVERT: B  338 GLU cc_start: 0.2526 (mm-30) cc_final: 0.2229 (mm-30)
REVERT: C  336 GLN cc_start: 0.8075 (mp10) cc_final: 0.7872 (mp10)
REVERT: C  338 GLU cc_start: 0.7689 (mp0) cc_final: 0.7111 (tm-30)
REVERT: C  349 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7292 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8201 (p0) cc_final: 0.7548 (p0)
REVERT: D  372 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: E  336 GLN cc_start: 0.8240 (mp10) cc_final: 0.7908 (mp10)
REVERT: E  343 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7522 (ttmm)
REVERT: E  348 ASP cc_start: 0.8150 (m-30) cc_final: 0.7508 (p0)
REVERT: E  372 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8147 (mm-30)
REVERT: E  379 ARG cc_start: 0.7589 (mtt180) cc_final: 0.6550 (ptt-90)
REVERT: F  338 GLU cc_start: 0.8074 (mp0) cc_final: 0.7786 (pm20)
REVERT: F  379 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6078 (mtm180)
  outliers start: 12
  outliers final: 9
  residues processed: 120
  average time/residue: 0.1040
  time to fit residues: 14.4218
Evaluate side-chains
  116 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 329 HIS
B 368 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.143931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.119566 restraints weight = 5450.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 3.08
r_work: 0.3823 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.5956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3576  Z= 0.115
  Angle     :  0.642   9.328   4782  Z= 0.300
  Chirality :  0.047   0.123    534
  Planarity :  0.003   0.022    612
  Dihedral  :  4.495  14.122    474
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.65 %
    Favored  : 77.61 %
  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: -3.54 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 379 
 TYR   0.015   0.002   TYR D 310 
 PHE   0.009   0.001   PHE F 346 
 HIS   0.003   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3576)
  covalent geometry    : angle       0.64171 ( 4782)
  hydrogen bonds       : bond        0.02147 (   33)
  hydrogen bonds       : angle       5.30567 (   99)

*********************** 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
  114 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8706 (mtmt) cc_final: 0.7984 (mmtm)
REVERT: A  317 LYS cc_start: 0.8549 (ptpt) cc_final: 0.7857 (ptpp)
REVERT: A  336 GLN cc_start: 0.7411 (mp10) cc_final: 0.7150 (tm-30)
REVERT: A  338 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6704 (tm-30)
REVERT: A  349 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7575 (mtm180)
REVERT: B  311 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8356 (mmtt)
REVERT: C  336 GLN cc_start: 0.8080 (mp10) cc_final: 0.7680 (mp10)
REVERT: C  338 GLU cc_start: 0.7712 (mp0) cc_final: 0.7033 (tm-30)
REVERT: C  341 SER cc_start: 0.8213 (m) cc_final: 0.7970 (t)
REVERT: C  349 ARG cc_start: 0.7578 (mtt-85) cc_final: 0.7102 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8193 (p0) cc_final: 0.7538 (p0)
REVERT: E  348 ASP cc_start: 0.8195 (m-30) cc_final: 0.7459 (p0)
REVERT: E  379 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6510 (ptt-90)
REVERT: F  311 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8606 (mtpt)
REVERT: F  370 LYS cc_start: 0.8787 (tptm) cc_final: 0.8574 (tptp)
  outliers start: 7
  outliers final: 5
  residues processed: 110
  average time/residue: 0.0929
  time to fit residues: 11.9206
Evaluate side-chains
  106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:   30.0000
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
F 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.142538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.118290 restraints weight = 5563.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 3.13
r_work: 0.3807 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.6235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3576  Z= 0.161
  Angle     :  0.644   7.476   4782  Z= 0.307
  Chirality :  0.047   0.126    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.497  13.359    474
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.14 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.51 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.014   0.002   TYR A 310 
 PHE   0.009   0.002   PHE D 378 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3576)
  covalent geometry    : angle       0.64440 ( 4782)
  hydrogen bonds       : bond        0.01973 (   33)
  hydrogen bonds       : angle       5.09969 (   99)

*********************** 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
  110 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8703 (mtmt) cc_final: 0.7934 (mmtm)
REVERT: A  317 LYS cc_start: 0.8558 (ptpt) cc_final: 0.7879 (ptpp)
REVERT: A  336 GLN cc_start: 0.7364 (mp10) cc_final: 0.7146 (tm-30)
REVERT: A  338 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6671 (tm-30)
REVERT: A  349 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7325 (mtm180)
REVERT: B  311 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8263 (mmtt)
REVERT: B  338 GLU cc_start: 0.2009 (mm-30) cc_final: 0.1500 (mm-30)
REVERT: C  336 GLN cc_start: 0.8051 (mp10) cc_final: 0.7829 (mp10)
REVERT: C  338 GLU cc_start: 0.7595 (mp0) cc_final: 0.6995 (tm-30)
REVERT: C  349 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7078 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8204 (p0) cc_final: 0.7687 (p0)
REVERT: D  336 GLN cc_start: 0.8339 (mp10) cc_final: 0.7759 (mp10)
REVERT: E  336 GLN cc_start: 0.8280 (mp10) cc_final: 0.8018 (mp10)
REVERT: E  342 GLU cc_start: 0.3257 (OUTLIER) cc_final: 0.2460 (pm20)
REVERT: E  348 ASP cc_start: 0.8199 (m-30) cc_final: 0.7442 (p0)
REVERT: E  379 ARG cc_start: 0.7415 (mtt180) cc_final: 0.6525 (ptt-90)
REVERT: F  380 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6777 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0937
  time to fit residues: 11.3542
Evaluate side-chains
  107 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    4.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
D 307 GLN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
F 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.138516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.114555 restraints weight = 5652.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 3.14
r_work: 0.3746 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.6683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3576  Z= 0.235
  Angle     :  0.695   7.310   4782  Z= 0.337
  Chirality :  0.048   0.133    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.899  14.207    474
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 23.63 %
    Favored  : 73.63 %
  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: -3.60 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 349 
 TYR   0.014   0.002   TYR A 310 
 PHE   0.015   0.002   PHE B 378 
 HIS   0.003   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 3576)
  covalent geometry    : angle       0.69469 ( 4782)
  hydrogen bonds       : bond        0.02550 (   33)
  hydrogen bonds       : angle       5.13642 (   99)

*********************** 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
  112 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8051 (mmtm)
REVERT: A  317 LYS cc_start: 0.8609 (ptpt) cc_final: 0.7980 (ptpp)
REVERT: A  338 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6528 (tm-30)
REVERT: A  349 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7148 (mtm180)
REVERT: B  311 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8243 (mmtt)
REVERT: C  336 GLN cc_start: 0.8074 (mp10) cc_final: 0.7818 (mp10)
REVERT: C  338 GLU cc_start: 0.7618 (mp0) cc_final: 0.6995 (tm-30)
REVERT: C  349 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7012 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8215 (p0) cc_final: 0.7620 (p0)
REVERT: E  342 GLU cc_start: 0.3193 (OUTLIER) cc_final: 0.2422 (pm20)
REVERT: E  348 ASP cc_start: 0.8170 (m-30) cc_final: 0.7426 (p0)
REVERT: E  379 ARG cc_start: 0.7637 (mtt180) cc_final: 0.6743 (ptt-90)
REVERT: F  311 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8650 (mtpt)
REVERT: F  316 SER cc_start: 0.9495 (p) cc_final: 0.9264 (p)
REVERT: F  327 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7592 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 106
  average time/residue: 0.1008
  time to fit residues: 12.3937
Evaluate side-chains
  104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain F residue  327 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0030
   chunk 35 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.4074

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** D 330 HIS ** 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 = 0.4224 r_free = 0.4224 target = 0.141586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.117941 restraints weight = 5508.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 3.04
r_work: 0.3821 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.6821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3576  Z= 0.127
  Angle     :  0.672   8.217   4782  Z= 0.324
  Chirality :  0.047   0.157    534
  Planarity :  0.003   0.023    612
  Dihedral  :  4.353  13.720    474
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 26.12 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.48 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.014   0.002   TYR D 310 
 PHE   0.009   0.001   PHE D 378 
 HIS   0.003   0.001   HIS F 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3576)
  covalent geometry    : angle       0.67241 ( 4782)
  hydrogen bonds       : bond        0.01940 (   33)
  hydrogen bonds       : angle       5.02666 (   99)

*********************** 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
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8707 (mtmt) cc_final: 0.7946 (mmtm)
REVERT: A  317 LYS cc_start: 0.8559 (ptpt) cc_final: 0.7903 (ptpp)
REVERT: A  338 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6431 (tm-30)
REVERT: A  349 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7175 (mtm180)
REVERT: B  311 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8224 (mmtt)
REVERT: C  336 GLN cc_start: 0.8202 (mp10) cc_final: 0.7774 (mp10)
REVERT: C  338 GLU cc_start: 0.7522 (mp0) cc_final: 0.7005 (tm-30)
REVERT: C  349 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.7016 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8199 (p0) cc_final: 0.7659 (p0)
REVERT: D  336 GLN cc_start: 0.7773 (mp10) cc_final: 0.7420 (mp-120)
REVERT: D  349 ARG cc_start: 0.5736 (tpm170) cc_final: 0.4883 (ttp-110)
REVERT: E  348 ASP cc_start: 0.8209 (m-30) cc_final: 0.7454 (p0)
REVERT: F  316 SER cc_start: 0.9392 (p) cc_final: 0.9152 (p)
REVERT: F  349 ARG cc_start: 0.2013 (ppt170) cc_final: 0.1530 (ppt170)
  outliers start: 8
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0857
  time to fit residues: 10.0522
Evaluate side-chains
  104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 GLN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.137885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.114472 restraints weight = 5386.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.96
r_work: 0.3772 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.6978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3576  Z= 0.197
  Angle     :  0.708   8.159   4782  Z= 0.339
  Chirality :  0.048   0.170    534
  Planarity :  0.003   0.025    612
  Dihedral  :  4.544  13.572    474
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.88 %
    Favored  : 72.64 %
  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: -3.55 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.015   0.003   TYR F 310 
 PHE   0.011   0.002   PHE B 378 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3576)
  covalent geometry    : angle       0.70826 ( 4782)
  hydrogen bonds       : bond        0.02319 (   33)
  hydrogen bonds       : angle       4.97430 (   99)

*********************** 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
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8065 (mmtm)
REVERT: A  317 LYS cc_start: 0.8614 (ptpt) cc_final: 0.7965 (ptpp)
REVERT: A  338 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6472 (tm-30)
REVERT: A  349 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7210 (mtm180)
REVERT: B  311 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8256 (mmtt)
REVERT: C  336 GLN cc_start: 0.8200 (mp10) cc_final: 0.7711 (mp10)
REVERT: C  338 GLU cc_start: 0.7521 (mp0) cc_final: 0.7036 (tm-30)
REVERT: C  349 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7065 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8256 (p0) cc_final: 0.7667 (p0)
REVERT: D  349 ARG cc_start: 0.5732 (tpm170) cc_final: 0.4998 (ttp-110)
REVERT: D  372 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7818 (mp0)
REVERT: E  342 GLU cc_start: 0.3202 (OUTLIER) cc_final: 0.2424 (pm20)
REVERT: E  348 ASP cc_start: 0.8223 (m-30) cc_final: 0.7455 (p0)
REVERT: F  316 SER cc_start: 0.9516 (p) cc_final: 0.9269 (p)
REVERT: F  327 ASN cc_start: 0.7943 (p0) cc_final: 0.7487 (p0)
REVERT: F  349 ARG cc_start: 0.2304 (ppt170) cc_final: 0.1807 (ppt170)
  outliers start: 10
  outliers final: 9
  residues processed: 100
  average time/residue: 0.0873
  time to fit residues: 10.2847
Evaluate side-chains
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 GLN
D 368 ASN
F 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.138788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.115596 restraints weight = 5513.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 3.00
r_work: 0.3786 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.7060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3576  Z= 0.164
  Angle     :  0.699   8.151   4782  Z= 0.334
  Chirality :  0.048   0.172    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.391  13.632    474
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 25.62 %
    Favored  : 72.14 %
  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: -3.52 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.016   0.003   TYR F 310 
 PHE   0.009   0.001   PHE D 378 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3576)
  covalent geometry    : angle       0.69935 ( 4782)
  hydrogen bonds       : bond        0.02142 (   33)
  hydrogen bonds       : angle       4.95859 (   99)

********************** 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
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8751 (mtmt) cc_final: 0.7997 (mmtm)
REVERT: A  317 LYS cc_start: 0.8622 (ptpt) cc_final: 0.7979 (ptpp)
REVERT: A  338 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6622 (tm-30)
REVERT: A  349 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7205 (mtm180)
REVERT: B  311 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8256 (mmtt)
REVERT: C  336 GLN cc_start: 0.8182 (mp10) cc_final: 0.7794 (mp10)
REVERT: C  338 GLU cc_start: 0.7519 (mp0) cc_final: 0.7022 (tm-30)
REVERT: C  349 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7060 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8298 (p0) cc_final: 0.7704 (p0)
REVERT: D  349 ARG cc_start: 0.5354 (tpm170) cc_final: 0.4877 (ttp-110)
REVERT: D  372 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7618 (mp0)
REVERT: D  380 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6801 (mp0)
REVERT: E  342 GLU cc_start: 0.3341 (OUTLIER) cc_final: 0.2518 (pm20)
REVERT: F  316 SER cc_start: 0.9466 (p) cc_final: 0.9215 (p)
REVERT: F  327 ASN cc_start: 0.7772 (p0) cc_final: 0.7376 (p0)
REVERT: F  349 ARG cc_start: 0.1966 (ppt170) cc_final: 0.1613 (ppt170)
  outliers start: 9
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0879
  time to fit residues: 10.4004
Evaluate side-chains
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 17 optimal weight:    0.1980
   chunk 24 optimal weight:   20.0000
   chunk 35 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 GLN
D 368 ASN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.143498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.120364 restraints weight = 5409.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.94
r_work: 0.3851 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.7052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3576  Z= 0.116
  Angle     :  0.666   8.627   4782  Z= 0.313
  Chirality :  0.047   0.175    534
  Planarity :  0.003   0.025    612
  Dihedral  :  3.937  12.787    474
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 26.37 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.38 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.017   0.003   TYR F 310 
 PHE   0.008   0.001   PHE D 378 
 HIS   0.002   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3576)
  covalent geometry    : angle       0.66607 ( 4782)
  hydrogen bonds       : bond        0.01470 (   33)
  hydrogen bonds       : angle       4.88218 (   99)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1063.04 seconds
wall clock time: 19 minutes 7.33 seconds (1147.33 seconds total)