Starting phenix.real_space_refine
on Wed Sep 17 04:30:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fof_50621/09_2025/9fof_50621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fof_50621/09_2025/9fof_50621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fof_50621/09_2025/9fof_50621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fof_50621/09_2025/9fof_50621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fof_50621/09_2025/9fof_50621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fof_50621/09_2025/9fof_50621.cif"
  }
  resolution = 2.9
  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=   0.004
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      60      5.16       5
     C    2538      2.51       5
     N     750      2.21       5
     O     828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 4176
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "q"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 431
          Classifications: {'peptide': 64}
          Link IDs: {'PTRANS': 1, 'TRANS': 62}
    Chain: "r"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 265
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
  Restraints were copied for chains:
    A, C, E, G, I, B, D, F, H, J
  Time building chain proxies: 0.82, per 1000 atoms: 0.20
  Number of scatterers: 4176
  At special positions: 0
  Unit cell: (68.8, 90.3, 54.18, 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      60     16.00
     O     828      8.00
     N     750      7.00
     C    2538      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: 0.40
  Conformation dependent library (CDL) restraints added in 215.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  936

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 35.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 302
      removed outlier: 3.515A  pdb=" N   ASN A 302 " --> pdb=" O   ASN C 301 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   ASN q 301 " --> pdb=" O   ASN C 302 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN q 302 " --> pdb=" O   ASN E 301 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN E 302 " --> pdb=" O   ASN G 301 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN G 302 " --> pdb=" O   ASN I 301 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 307
      removed outlier: 6.033A  pdb=" N   SER q 305 " --> pdb=" O   ASN C 306 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 312
      removed outlier: 6.291A  pdb=" N   MET q 311 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 318
      removed outlier: 7.297A  pdb=" N   SER q 317 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324
      removed outlier: 7.379A  pdb=" N   MET q 323 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 337
      removed outlier: 3.500A  pdb=" N   TRP C 334 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   MET C 336 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   MET A 337 " --> pdb=" O   MET C 336 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ALA q 328 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   GLN C 331 " --> pdb=" O   ALA q 328 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LEU q 330 " --> pdb=" O   GLN C 331 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   SER C 333 " --> pdb=" O   LEU q 330 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   SER q 332 " --> pdb=" O   SER C 333 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLY C 335 " --> pdb=" O   SER q 332 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   TRP q 334 " --> pdb=" O   GLY C 335 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   MET C 337 " --> pdb=" O   TRP q 334 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   MET q 336 " --> pdb=" O   MET C 337 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TRP E 334 " --> pdb=" O   SER q 333 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   MET E 336 " --> pdb=" O   GLY q 335 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   MET q 337 " --> pdb=" O   MET E 336 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TRP G 334 " --> pdb=" O   SER E 333 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   MET G 336 " --> pdb=" O   GLY E 335 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   MET E 337 " --> pdb=" O   MET G 336 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TRP I 334 " --> pdb=" O   SER G 333 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   MET I 336 " --> pdb=" O   GLY G 335 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   MET G 337 " --> pdb=" O   MET I 336 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 343
      removed outlier: 7.316A  pdb=" N   SER A 342 " --> pdb=" O   GLN C 343 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   SER q 342 " --> pdb=" O   GLN E 343 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   SER E 342 " --> pdb=" O   GLN G 343 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   SER G 342 " --> pdb=" O   GLN I 343 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 50
      removed outlier: 3.564A  pdb=" N   GLY D  47 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE D  49 " --> pdb=" O   GLN B  48 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ASN B  50 " --> pdb=" O   PHE D  49 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   ASN r  41 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   THR D  44 " --> pdb=" O   ASN r  41 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ALA r  43 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   ALA D  46 " --> pdb=" O   ALA r  43 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   TYR r  45 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   GLN D  48 " --> pdb=" O   TYR r  45 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   GLY r  47 " --> pdb=" O   GLN D  48 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   ASN D  50 " --> pdb=" O   GLY r  47 " (cutoff:3.500A)
      removed outlier: 9.048A  pdb=" N   PHE r  49 " --> pdb=" O   ASN D  50 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY F  47 " --> pdb=" O   ALA r  46 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE F  49 " --> pdb=" O   GLN r  48 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ASN r  50 " --> pdb=" O   PHE F  49 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY H  47 " --> pdb=" O   ALA F  46 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE H  49 " --> pdb=" O   GLN F  48 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ASN F  50 " --> pdb=" O   PHE H  49 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY J  47 " --> pdb=" O   ALA H  46 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE J  49 " --> pdb=" O   GLN H  48 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ASN H  50 " --> pdb=" O   PHE J  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 65
      removed outlier: 6.402A  pdb=" N   ALA B  58 " --> pdb=" O   ALA D  59 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   MET D  61 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ASN B  60 " --> pdb=" O   MET D  61 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   GLY D  63 " --> pdb=" O   ASN B  60 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   SER B  62 " --> pdb=" O   GLY D  63 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   PHE D  65 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   THR B  64 " --> pdb=" O   PHE D  65 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ALA r  58 " --> pdb=" O   ALA F  59 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   MET F  61 " --> pdb=" O   ALA r  58 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ASN r  60 " --> pdb=" O   MET F  61 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   GLY F  63 " --> pdb=" O   ASN r  60 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   SER r  62 " --> pdb=" O   GLY F  63 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   PHE F  65 " --> pdb=" O   SER r  62 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   THR r  64 " --> pdb=" O   PHE F  65 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ALA F  58 " --> pdb=" O   ALA H  59 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   MET H  61 " --> pdb=" O   ALA F  58 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ASN F  60 " --> pdb=" O   MET H  61 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY H  63 " --> pdb=" O   ASN F  60 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   SER F  62 " --> pdb=" O   GLY H  63 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE H  65 " --> pdb=" O   SER F  62 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   THR F  64 " --> pdb=" O   PHE H  65 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ALA H  58 " --> pdb=" O   ALA J  59 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   MET J  61 " --> pdb=" O   ALA H  58 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ASN H  60 " --> pdb=" O   MET J  61 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLY J  63 " --> pdb=" O   ASN H  60 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   SER H  62 " --> pdb=" O   GLY J  63 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE J  65 " --> pdb=" O   SER H  62 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   THR H  64 " --> pdb=" O   PHE J  65 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 73
      removed outlier: 5.926A  pdb=" N   ASN B  72 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   ASN r  72 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   ASN F  72 " --> pdb=" O   LEU H  73 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   ASN H  72 " --> pdb=" O   LEU J  73 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    246 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: 0.59

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 891
        1.34 -     1.45: 1053
        1.45 -     1.57: 2178
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 4242
  Sorted by residual:
  bond pdb=" C   MET H  70 "
       pdb=" N   PRO H  71 "
    ideal  model  delta    sigma   weight residual
    1.333  1.363 -0.030 1.17e-02 7.31e+03 6.58e+00
  bond pdb=" C   MET J  70 "
       pdb=" N   PRO J  71 "
    ideal  model  delta    sigma   weight residual
    1.333  1.363 -0.030 1.17e-02 7.31e+03 6.50e+00
  bond pdb=" C   MET B  70 "
       pdb=" N   PRO B  71 "
    ideal  model  delta    sigma   weight residual
    1.333  1.362 -0.030 1.17e-02 7.31e+03 6.47e+00
  bond pdb=" C   MET F  70 "
       pdb=" N   PRO F  71 "
    ideal  model  delta    sigma   weight residual
    1.333  1.362 -0.030 1.17e-02 7.31e+03 6.47e+00
  bond pdb=" C   ASN J  69 "
       pdb=" N   MET J  70 "
    ideal  model  delta    sigma   weight residual
    1.332  1.354 -0.022 8.60e-03 1.35e+04 6.40e+00
  ... (remaining 4237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 3223
        1.15 -     2.30: 1728
        2.30 -     3.44: 538
        3.44 -     4.59: 129
        4.59 -     5.74: 52
  Bond angle restraints: 5670
  Sorted by residual:
  angle pdb=" CA  ASP J  52 "
        pdb=" CB  ASP J  52 "
        pdb=" CG  ASP J  52 "
      ideal   model   delta    sigma   weight residual
     112.60  117.50   -4.90 1.00e+00 1.00e+00 2.40e+01
  angle pdb=" CA  ASP F  52 "
        pdb=" CB  ASP F  52 "
        pdb=" CG  ASP F  52 "
      ideal   model   delta    sigma   weight residual
     112.60  117.49   -4.89 1.00e+00 1.00e+00 2.39e+01
  angle pdb=" CA  ASP B  52 "
        pdb=" CB  ASP B  52 "
        pdb=" CG  ASP B  52 "
      ideal   model   delta    sigma   weight residual
     112.60  117.48   -4.88 1.00e+00 1.00e+00 2.38e+01
  angle pdb=" CA  ASP r  52 "
        pdb=" CB  ASP r  52 "
        pdb=" CG  ASP r  52 "
      ideal   model   delta    sigma   weight residual
     112.60  117.47   -4.87 1.00e+00 1.00e+00 2.37e+01
  angle pdb=" CA  ASP D  52 "
        pdb=" CB  ASP D  52 "
        pdb=" CG  ASP D  52 "
      ideal   model   delta    sigma   weight residual
     112.60  117.45   -4.85 1.00e+00 1.00e+00 2.35e+01
  ... (remaining 5665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.35: 2124
       14.35 -    28.71: 192
       28.71 -    43.06: 36
       43.06 -    57.41: 12
       57.41 -    71.76: 18
  Dihedral angle restraints: 2382
    sinusoidal: 840
      harmonic: 1542
  Sorted by residual:
  dihedral pdb=" N   GLN J  48 "
           pdb=" C   GLN J  48 "
           pdb=" CA  GLN J  48 "
           pdb=" CB  GLN J  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.22  -10.42     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" N   GLN D  48 "
           pdb=" C   GLN D  48 "
           pdb=" CA  GLN D  48 "
           pdb=" CB  GLN D  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.22  -10.42     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" N   GLN F  48 "
           pdb=" C   GLN F  48 "
           pdb=" CA  GLN F  48 "
           pdb=" CB  GLN F  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.22  -10.42     0      2.50e+00 1.60e-01 1.74e+01
  ... (remaining 2379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 378
       0.073 -    0.147: 114
       0.147 -    0.220: 24
       0.220 -    0.293: 6
       0.293 -    0.366: 6
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  GLN B  48 "
            pdb=" N   GLN B  48 "
            pdb=" C   GLN B  48 "
            pdb=" CB  GLN B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CA  GLN r  48 "
            pdb=" N   GLN r  48 "
            pdb=" C   GLN r  48 "
            pdb=" CB  GLN r  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.37 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  GLN F  48 "
            pdb=" N   GLN F  48 "
            pdb=" C   GLN F  48 "
            pdb=" CB  GLN F  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.37 2.00e-01 2.50e+01 3.33e+00
  ... (remaining 525 not shown)

  Planarity restraints: 804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G 334 "    0.024 2.00e-02 2.50e+03   1.26e-02 3.95e+00
        pdb=" CG  TRP G 334 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP G 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP G 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP G 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP G 334 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP G 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G 334 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP G 334 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 334 "    0.024 2.00e-02 2.50e+03   1.25e-02 3.88e+00
        pdb=" CG  TRP A 334 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 334 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 334 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 334 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 334 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 334 "    0.024 2.00e-02 2.50e+03   1.24e-02 3.87e+00
        pdb=" CG  TRP E 334 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 334 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 334 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 334 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 334 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 334 "    0.004 2.00e-02 2.50e+03
  ... (remaining 801 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 936
        2.85 -     3.36: 3471
        3.36 -     3.87: 6871
        3.87 -     4.39: 7620
        4.39 -     4.90: 13174
  Nonbonded interactions: 32072
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN q 286 "
            pdb=" O   SER E 292 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" NE2 GLN A 286 "
            pdb=" O   SER C 292 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" NE2 GLN G 286 "
            pdb=" O   SER I 292 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" O   SER q 292 "
            pdb=" NE2 GLN C 286 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" NE2 GLN E 286 "
            pdb=" O   SER G 292 "
     model   vdw
     2.333 3.120
  ... (remaining 32067 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'q'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'r'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
}

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:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.160
  Find NCS groups from input model:        0.050
  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:7.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   15.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5473
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   0.033   4242  Z= 0.792
  Angle     :  1.531   5.741   5670  Z= 1.029
  Chirality :  0.084   0.366    528
  Planarity :  0.008   0.064    804
  Dihedral  : 13.929  71.764   1446
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  4.17 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  1.56 %
    Favored  : 96.88 %
  Cbeta Deviations :  1.28 %
  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: -4.04 (0.20), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.15), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.005   ARG E 293 
 TYR   0.004   0.001   TYR J  53 
 PHE   0.015   0.004   PHE I 313 
 TRP   0.028   0.009   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01137 ( 4242)
  covalent geometry    : angle       1.53147 ( 5670)
  hydrogen bonds       : bond        0.32520 (   82)
  hydrogen bonds       : angle      12.82716 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: q  303 GLN cc_start: 0.8263 (mt0) cc_final: 0.7852 (mt0)
REVERT: q  323 MET cc_start: 0.8369 (ttm) cc_final: 0.8073 (ttm)
REVERT: r   70 MET cc_start: 0.7813 (mtp) cc_final: 0.6951 (ttp)
REVERT: B   70 MET cc_start: 0.6459 (mtp) cc_final: 0.5856 (mmt)
REVERT: C  307 MET cc_start: 0.6424 (tpt) cc_final: 0.6135 (tmt)
REVERT: D   53 TYR cc_start: 0.6512 (m-80) cc_final: 0.6227 (m-80)
REVERT: D   70 MET cc_start: 0.7314 (mtp) cc_final: 0.6443 (mmm)
  outliers start: 6
  outliers final: 1
  residues processed: 110
  average time/residue: 0.5013
  time to fit residues: 57.0147
Evaluate side-chains
  92 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  319 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
q 345 ASN
A 285 ASN
A 319 ASN
C 286 GLN
C 302 ASN
D  69 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
G 285 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.219173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.198653 restraints weight = 4853.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.4694 rms_B_bonded: 1.60
r_work: 0.4622 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.4498 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.4498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4242  Z= 0.153
  Angle     :  0.746   7.163   5670  Z= 0.396
  Chirality :  0.041   0.167    528
  Planarity :  0.005   0.042    804
  Dihedral  :  6.260  24.530    614
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 12.24 %
    Favored  : 84.11 %
  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: -4.03 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 293 
 TYR   0.009   0.001   TYR J  45 
 PHE   0.012   0.002   PHE r  49 
 TRP   0.017   0.003   TRP I 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4242)
  covalent geometry    : angle       0.74591 ( 5670)
  hydrogen bonds       : bond        0.03952 (   82)
  hydrogen bonds       : angle       6.78990 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.090 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8094 (mt0) cc_final: 0.7734 (mt0)
REVERT: C  299 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6286 (tt)
REVERT: E  299 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: G  307 MET cc_start: 0.6252 (mpm) cc_final: 0.5938 (mtm)
REVERT: G  322 MET cc_start: 0.6901 (ttt) cc_final: 0.5924 (ttt)
  outliers start: 14
  outliers final: 1
  residues processed: 111
  average time/residue: 0.5458
  time to fit residues: 62.6719
Evaluate side-chains
  96 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain E residue  299 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 18 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
q 286 GLN
A 286 GLN
C 285 ASN
C 291 ASN
F  41 ASN
F  60 ASN
H  51 GLN
I 285 ASN
** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.150817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.135424 restraints weight = 4774.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 1.33
r_work: 0.3978 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3867 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.9995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4242  Z= 0.196
  Angle     :  0.856   8.358   5670  Z= 0.461
  Chirality :  0.041   0.184    528
  Planarity :  0.004   0.040    804
  Dihedral  :  6.719  24.859    612
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 16.41 %
    Favored  : 79.17 %
  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: -4.24 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG I 293 
 TYR   0.013   0.002   TYR B  45 
 PHE   0.021   0.002   PHE J  65 
 TRP   0.015   0.003   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4242)
  covalent geometry    : angle       0.85622 ( 5670)
  hydrogen bonds       : bond        0.07198 (   82)
  hydrogen bonds       : angle       6.35018 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.122 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8428 (mt0) cc_final: 0.8131 (mt0)
REVERT: A  337 MET cc_start: 0.8544 (ttp) cc_final: 0.8332 (ttt)
REVERT: C  337 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8403 (mtp)
REVERT: G  323 MET cc_start: 0.7274 (ttt) cc_final: 0.7029 (ttt)
REVERT: J   57 MET cc_start: 0.5092 (tmt) cc_final: 0.4778 (ttm)
  outliers start: 17
  outliers final: 3
  residues processed: 124
  average time/residue: 0.5284
  time to fit residues: 67.8745
Evaluate side-chains
  103 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 MET
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 31 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
q 319 ASN
A 285 ASN
A 345 ASN
B  50 ASN
C 303 GLN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 319 ASN
F  60 ASN
G 285 ASN
G 286 GLN
** I 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.111623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.100647 restraints weight = 5280.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.42
r_work: 0.3398 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          1.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   4242  Z= 0.243
  Angle     :  0.931   7.634   5670  Z= 0.511
  Chirality :  0.045   0.227    528
  Planarity :  0.005   0.044    804
  Dihedral  :  6.400  18.084    612
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.01 %
    Favored  : 77.34 %
  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: -4.43 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.13), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG I 293 
 TYR   0.017   0.002   TYR F  45 
 PHE   0.042   0.003   PHE E 289 
 TRP   0.020   0.003   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 4242)
  covalent geometry    : angle       0.93057 ( 5670)
  hydrogen bonds       : bond        0.07542 (   82)
  hydrogen bonds       : angle       5.79376 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.161 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8531 (mt0) cc_final: 0.8170 (mt0)
REVERT: A  292 SER cc_start: 0.8856 (t) cc_final: 0.8455 (t)
REVERT: C  292 SER cc_start: 0.9176 (p) cc_final: 0.8972 (p)
REVERT: D   70 MET cc_start: 0.7837 (ttm) cc_final: 0.7559 (ttt)
REVERT: G  323 MET cc_start: 0.8147 (ttt) cc_final: 0.7886 (ttm)
REVERT: H   53 TYR cc_start: 0.8482 (m-80) cc_final: 0.8111 (m-80)
REVERT: I  344 GLN cc_start: 0.7600 (mt0) cc_final: 0.7329 (mt0)
  outliers start: 14
  outliers final: 2
  residues processed: 120
  average time/residue: 0.5821
  time to fit residues: 72.1152
Evaluate side-chains
  113 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain E residue  319 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  50 ASN
C 303 GLN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 319 ASN
F  60 ASN
J  50 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.105231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.095452 restraints weight = 5514.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.45
r_work: 0.3283 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          1.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4242  Z= 0.187
  Angle     :  0.790   6.225   5670  Z= 0.429
  Chirality :  0.042   0.164    528
  Planarity :  0.004   0.044    804
  Dihedral  :  5.940  17.546    612
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.79 %
    Favored  : 76.30 %
  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: -4.46 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG I 293 
 TYR   0.014   0.002   TYR H  74 
 PHE   0.013   0.002   PHE E 289 
 TRP   0.019   0.003   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4242)
  covalent geometry    : angle       0.78980 ( 5670)
  hydrogen bonds       : bond        0.06566 (   82)
  hydrogen bonds       : angle       5.36539 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.153 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8451 (mt0) cc_final: 0.8081 (mt0)
REVERT: C  292 SER cc_start: 0.9116 (p) cc_final: 0.8861 (p)
REVERT: G  289 PHE cc_start: 0.7350 (t80) cc_final: 0.7004 (t80)
  outliers start: 15
  outliers final: 2
  residues processed: 119
  average time/residue: 0.5378
  time to fit residues: 66.2899
Evaluate side-chains
  108 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain E residue  299 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
B  60 ASN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
J  51 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.093750 restraints weight = 5512.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.44
r_work: 0.3221 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          1.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4242  Z= 0.155
  Angle     :  0.725   6.071   5670  Z= 0.396
  Chirality :  0.040   0.169    528
  Planarity :  0.004   0.045    804
  Dihedral  :  5.684  15.197    612
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.27 %
    Favored  : 77.86 %
  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: -4.51 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG I 293 
 TYR   0.015   0.002   TYR J  74 
 PHE   0.016   0.002   PHE E 289 
 TRP   0.018   0.003   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4242)
  covalent geometry    : angle       0.72478 ( 5670)
  hydrogen bonds       : bond        0.06171 (   82)
  hydrogen bonds       : angle       5.30784 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.095 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8442 (mt0) cc_final: 0.8076 (mt0)
REVERT: B   70 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7656 (mmm)
REVERT: C  292 SER cc_start: 0.9193 (p) cc_final: 0.8950 (p)
REVERT: G  289 PHE cc_start: 0.7347 (t80) cc_final: 0.7013 (t80)
  outliers start: 11
  outliers final: 3
  residues processed: 120
  average time/residue: 0.4874
  time to fit residues: 60.5927
Evaluate side-chains
  112 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    8.3990

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

Flipped N/Q/H residues before XYZ refinement:
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 GLN
A 319 ASN
B  50 ASN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
H  50 ASN
J  50 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.096815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.087367 restraints weight = 5720.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.43
r_work: 0.3129 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          1.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   4242  Z= 0.323
  Angle     :  1.012  11.553   5670  Z= 0.550
  Chirality :  0.050   0.224    528
  Planarity :  0.005   0.052    804
  Dihedral  :  6.317  16.450    612
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.79 %
    Favored  : 76.56 %
  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: -4.69 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 293 
 TYR   0.022   0.003   TYR F  45 
 PHE   0.019   0.004   PHE H  49 
 TRP   0.020   0.004   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 ( 4242)
  covalent geometry    : angle       1.01220 ( 5670)
  hydrogen bonds       : bond        0.09592 (   82)
  hydrogen bonds       : angle       6.00697 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.140 
Fit side-chains
REVERT: r   61 MET cc_start: 0.8733 (mtm) cc_final: 0.8499 (mtm)
REVERT: B   70 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7723 (mmm)
REVERT: C  292 SER cc_start: 0.9209 (p) cc_final: 0.8976 (p)
REVERT: G  299 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8301 (tp)
  outliers start: 14
  outliers final: 4
  residues processed: 117
  average time/residue: 0.5218
  time to fit residues: 63.1358
Evaluate side-chains
  111 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain G residue  299 LEU
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
q 303 GLN
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
B  50 ASN
C 306 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
J  50 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.102600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.093043 restraints weight = 5506.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.43
r_work: 0.3227 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          1.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4242  Z= 0.120
  Angle     :  0.681  10.087   5670  Z= 0.367
  Chirality :  0.038   0.161    528
  Planarity :  0.004   0.049    804
  Dihedral  :  5.490  15.191    612
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.66 %
    Favored  : 75.26 %
  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: -4.65 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.53 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 293 
 TYR   0.007   0.001   TYR F  45 
 PHE   0.017   0.002   PHE C 289 
 TRP   0.019   0.003   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4242)
  covalent geometry    : angle       0.68063 ( 5670)
  hydrogen bonds       : bond        0.04939 (   82)
  hydrogen bonds       : angle       5.23518 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.100 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8508 (mt0) cc_final: 0.8125 (mt0)
REVERT: B   70 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7681 (mmm)
REVERT: C  292 SER cc_start: 0.9133 (p) cc_final: 0.8907 (p)
REVERT: E  299 LEU cc_start: 0.8455 (tm) cc_final: 0.8250 (tp)
  outliers start: 8
  outliers final: 3
  residues processed: 111
  average time/residue: 0.4736
  time to fit residues: 54.4127
Evaluate side-chains
  106 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain E residue  340 LEU
Chi-restraints excluded: chain F residue   61 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 13 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 303 GLN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
H  50 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.098720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.088930 restraints weight = 5609.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.47
r_work: 0.3163 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          1.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4242  Z= 0.222
  Angle     :  0.847  11.245   5670  Z= 0.458
  Chirality :  0.044   0.217    528
  Planarity :  0.004   0.047    804
  Dihedral  :  5.887  15.771    612
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 22.92 %
    Favored  : 75.26 %
  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: -4.71 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 293 
 TYR   0.016   0.002   TYR F  45 
 PHE   0.021   0.003   PHE I 289 
 TRP   0.018   0.004   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 4242)
  covalent geometry    : angle       0.84728 ( 5670)
  hydrogen bonds       : bond        0.07839 (   82)
  hydrogen bonds       : angle       5.64917 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B   70 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7616 (mmm)
REVERT: C  292 SER cc_start: 0.9179 (p) cc_final: 0.8957 (p)
REVERT: G  289 PHE cc_start: 0.7489 (t80) cc_final: 0.7002 (m-80)
REVERT: J   55 SER cc_start: 0.8978 (t) cc_final: 0.8727 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 109
  average time/residue: 0.5101
  time to fit residues: 57.5570
Evaluate side-chains
  112 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain E residue  340 LEU
Chi-restraints excluded: chain F residue   61 MET
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0970
   chunk 4 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   overall best weight:    3.3584

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

Flipped N/Q/H residues before XYZ refinement:
q 303 GLN
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 306 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
H  50 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.100460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.090761 restraints weight = 5476.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.45
r_work: 0.3192 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          1.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4242  Z= 0.159
  Angle     :  0.747   9.896   5670  Z= 0.404
  Chirality :  0.041   0.189    528
  Planarity :  0.004   0.050    804
  Dihedral  :  5.601  15.423    612
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.92 %
    Favored  : 75.00 %
  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: -4.72 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 293 
 TYR   0.011   0.001   TYR H  74 
 PHE   0.021   0.002   PHE I 289 
 TRP   0.018   0.003   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4242)
  covalent geometry    : angle       0.74705 ( 5670)
  hydrogen bonds       : bond        0.06274 (   82)
  hydrogen bonds       : angle       5.40316 (  246)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.157 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8451 (mt0) cc_final: 0.8064 (mt0)
REVERT: A  292 SER cc_start: 0.8920 (t) cc_final: 0.8554 (t)
REVERT: B   70 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7645 (mmm)
REVERT: G  289 PHE cc_start: 0.7481 (t80) cc_final: 0.6975 (m-80)
REVERT: J   55 SER cc_start: 0.8976 (t) cc_final: 0.8727 (t)
  outliers start: 8
  outliers final: 3
  residues processed: 107
  average time/residue: 0.5124
  time to fit residues: 56.6941
Evaluate side-chains
  107 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain E residue  340 LEU
Chi-restraints excluded: chain F residue   61 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 306 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  60 ASN
H  50 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.100617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.090730 restraints weight = 5562.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.48
r_work: 0.3191 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          1.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4242  Z= 0.157
  Angle     :  0.740   8.939   5670  Z= 0.401
  Chirality :  0.041   0.183    528
  Planarity :  0.004   0.050    804
  Dihedral  :  5.558  15.322    612
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.92 %
    Favored  : 75.00 %
  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: -4.71 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 293 
 TYR   0.012   0.001   TYR F  45 
 PHE   0.021   0.002   PHE I 289 
 TRP   0.018   0.003   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4242)
  covalent geometry    : angle       0.73965 ( 5670)
  hydrogen bonds       : bond        0.06293 (   82)
  hydrogen bonds       : angle       5.35992 (  246)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.71 seconds
wall clock time: 29 minutes 44.57 seconds (1784.57 seconds total)