Starting phenix.real_space_refine
on Thu Mar  6 00:08:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fof_50621/03_2025/9fof_50621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fof_50621/03_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_50621/03_2025/9fof_50621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fof_50621/03_2025/9fof_50621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fof_50621/03_2025/9fof_50621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fof_50621/03_2025/9fof_50621.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4176
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      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: "B"
      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:
    D, F, H, J, r, C, E, G, I, q
  Time building chain proxies: 5.83, per 1000 atoms: 1.40
  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: 0.96
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.67
  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: 2.05

  Time building geometry restraints manager: 1.23 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'r'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'q'
}

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:             271.500
  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:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     24.810
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.090
  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:             0.010
  Load rotamer database and sin/cos tables:54.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  351.410
-------------------------------------------------------------------------------
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= 0.755
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.028   0.009   TRP G 334 
 PHE   0.015   0.004   PHE I 313 
 TYR   0.004   0.001   TYR J  53 
 ARG   0.011   0.005   ARG E 293 

*********************** 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  : 0.506 
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: 1.3854
  time to fit residues: 158.1174
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  : 0.412 
-------------------------------------------------------------------------------
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 45 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4967 r_free = 0.4967 target = 0.219901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.199236 restraints weight = 4808.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4702 rms_B_bonded: 1.60
r_work: 0.4631 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.4505 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4242  Z= 0.212
  Angle     :  0.730   7.350   5670  Z= 0.390
  Chirality :  0.040   0.163    528
  Planarity :  0.004   0.040    804
  Dihedral  :  6.274  24.305    614
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 12.50 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP I 334 
 PHE   0.013   0.002   PHE r  49 
 TYR   0.009   0.001   TYR J  45 
 ARG   0.005   0.001   ARG E 293 

*********************** 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
  123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.448 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8076 (mt0) cc_final: 0.7726 (mt0)
REVERT: C  299 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6269 (tt)
REVERT: E  299 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7913 (mm)
REVERT: G  307 MET cc_start: 0.6349 (mpm) cc_final: 0.5945 (mtm)
REVERT: G  322 MET cc_start: 0.6924 (ttt) cc_final: 0.5955 (ttt)
  outliers start: 14
  outliers final: 1
  residues processed: 113
  average time/residue: 1.5956
  time to fit residues: 186.0785
Evaluate side-chains
  99 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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 21 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
q 286 GLN
** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r  50 ASN
A 286 GLN
C 285 ASN
C 291 ASN
C 302 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  41 ASN
F  60 ASN
G 285 ASN
** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  51 GLN
I 285 ASN
I 312 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.131930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.118862 restraints weight = 4988.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.36
r_work: 0.3700 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          1.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   4242  Z= 0.357
  Angle     :  1.020   9.682   5670  Z= 0.551
  Chirality :  0.047   0.178    528
  Planarity :  0.006   0.059    804
  Dihedral  :  7.323  23.887    612
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 16.41 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.41 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.13), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP E 334 
 PHE   0.018   0.003   PHE J  65 
 TYR   0.017   0.002   TYR J  74 
 ARG   0.003   0.001   ARG E 293 

*********************** 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
  149 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.402 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8487 (mt0) cc_final: 0.8138 (mt0)
REVERT: q  307 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7737 (tmt)
REVERT: r   61 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8488 (mtm)
REVERT: A  336 MET cc_start: 0.8495 (mtm) cc_final: 0.8291 (mtm)
REVERT: C  299 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8427 (tt)
REVERT: C  337 MET cc_start: 0.8661 (ttm) cc_final: 0.8449 (mtp)
REVERT: E  299 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8451 (tm)
REVERT: H   74 TYR cc_start: 0.7215 (t80) cc_final: 0.6021 (m-10)
REVERT: J   57 MET cc_start: 0.5691 (tmt) cc_final: 0.5373 (ttm)
  outliers start: 18
  outliers final: 4
  residues processed: 134
  average time/residue: 1.0151
  time to fit residues: 141.2395
Evaluate side-chains
  120 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  307 MET
Chi-restraints excluded: chain r residue   61 MET
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain E residue  319 ASN
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain H 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 4 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 27 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 GLN
B  72 ASN
C 303 GLN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 327 GLN
F  60 ASN
G 286 GLN
I 312 ASN
I 319 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.110535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.099786 restraints weight = 5153.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.38
r_work: 0.3362 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          1.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4242  Z= 0.305
  Angle     :  0.906   8.856   5670  Z= 0.494
  Chirality :  0.046   0.224    528
  Planarity :  0.005   0.045    804
  Dihedral  :  6.221  21.269    612
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.49 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.13), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP G 334 
 PHE   0.024   0.003   PHE E 289 
 TYR   0.014   0.002   TYR F  45 
 ARG   0.001   0.000   ARG G 293 

*********************** 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
  135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.418 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8535 (mt0) cc_final: 0.8213 (mt0)
REVERT: A  292 SER cc_start: 0.8946 (t) cc_final: 0.8613 (t)
REVERT: D   70 MET cc_start: 0.7636 (ttm) cc_final: 0.7402 (ttt)
REVERT: F   70 MET cc_start: 0.8152 (ttm) cc_final: 0.7923 (ttp)
REVERT: I  339 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.5493 (tpt)
REVERT: J   53 TYR cc_start: 0.8147 (m-80) cc_final: 0.7945 (m-80)
  outliers start: 13
  outliers final: 1
  residues processed: 126
  average time/residue: 1.1513
  time to fit residues: 150.4617
Evaluate side-chains
  114 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain I residue  339 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 49 optimal weight:    8.9990
   chunk 42 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   overall best weight:    9.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 303 GLN
A 319 ASN
A 344 GLN
B  60 ASN
C 303 GLN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 327 GLN
H  50 ASN
H  72 ASN
I 319 ASN
J  51 GLN
J  60 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.096776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.087162 restraints weight = 5745.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.47
r_work: 0.3126 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          1.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   4242  Z= 0.494
  Angle     :  1.069  10.637   5670  Z= 0.586
  Chirality :  0.052   0.214    528
  Planarity :  0.005   0.048    804
  Dihedral  :  6.637  18.286    612
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 20.05 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.61 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.51 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.005   TRP G 334 
 PHE   0.040   0.004   PHE E 289 
 TYR   0.023   0.003   TYR F  45 
 ARG   0.002   0.001   ARG I 293 

*********************** 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
  137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.386 
Fit side-chains
REVERT: C  292 SER cc_start: 0.9085 (p) cc_final: 0.8751 (p)
REVERT: D   70 MET cc_start: 0.7690 (ttm) cc_final: 0.7482 (ttt)
REVERT: F   70 MET cc_start: 0.8272 (ttm) cc_final: 0.8043 (ttp)
REVERT: G  299 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8325 (tp)
  outliers start: 16
  outliers final: 5
  residues processed: 124
  average time/residue: 1.0706
  time to fit residues: 137.7267
Evaluate side-chains
  116 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  292 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain G residue  299 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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**
r  48 GLN
A 319 ASN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  50 ASN
J  50 ASN
J  72 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.098712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.089018 restraints weight = 5626.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.45
r_work: 0.3158 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          1.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4242  Z= 0.277
  Angle     :  0.834   7.657   5670  Z= 0.455
  Chirality :  0.044   0.172    528
  Planarity :  0.004   0.045    804
  Dihedral  :  6.105  16.764    612
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 20.83 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.66 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP G 334 
 PHE   0.015   0.003   PHE H  49 
 TYR   0.014   0.002   TYR F  45 
 ARG   0.001   0.000   ARG I 293 

*********************** 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
  130 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.387 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8526 (mt0) cc_final: 0.8175 (mt0)
REVERT: A  292 SER cc_start: 0.8950 (t) cc_final: 0.8580 (t)
REVERT: C  292 SER cc_start: 0.9046 (p) cc_final: 0.8780 (p)
REVERT: G  289 PHE cc_start: 0.7260 (t80) cc_final: 0.7037 (t80)
  outliers start: 18
  outliers final: 4
  residues processed: 118
  average time/residue: 1.0127
  time to fit residues: 123.9360
Evaluate side-chains
  115 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  292 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 29 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0670
   chunk 31 optimal weight:   20.0000
   chunk 45 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   overall best weight:    6.4126

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.097744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.088183 restraints weight = 5632.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.44
r_work: 0.3136 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          1.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4242  Z= 0.353
  Angle     :  0.906  10.711   5670  Z= 0.494
  Chirality :  0.046   0.206    528
  Planarity :  0.004   0.051    804
  Dihedral  :  6.234  16.875    612
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.14 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.75 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP G 334 
 PHE   0.018   0.003   PHE H  49 
 TYR   0.017   0.002   TYR F  45 
 ARG   0.001   0.000   ARG I 293 

*********************** 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: 16
    poor density    : 110
  time to evaluate  : 0.422 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8495 (mt0) cc_final: 0.8182 (mt0)
REVERT: C  292 SER cc_start: 0.9076 (p) cc_final: 0.8761 (p)
  outliers start: 16
  outliers final: 6
  residues processed: 113
  average time/residue: 1.0777
  time to fit residues: 126.1756
Evaluate side-chains
  115 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  292 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain D residue   61 MET
Chi-restraints excluded: chain F residue   64 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 27 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 50 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    5.7990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.098686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.089104 restraints weight = 5625.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.43
r_work: 0.3150 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          1.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4242  Z= 0.325
  Angle     :  0.879  11.103   5670  Z= 0.478
  Chirality :  0.045   0.203    528
  Planarity :  0.004   0.051    804
  Dihedral  :  6.147  16.819    612
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.44 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.76 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP G 334 
 PHE   0.016   0.003   PHE H  49 
 TYR   0.016   0.002   TYR F  45 
 ARG   0.001   0.000   ARG I 293 

*********************** 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
  121 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.390 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8476 (mt0) cc_final: 0.8159 (mt0)
REVERT: A  292 SER cc_start: 0.8936 (t) cc_final: 0.8566 (t)
REVERT: C  292 SER cc_start: 0.9063 (p) cc_final: 0.8806 (p)
  outliers start: 12
  outliers final: 7
  residues processed: 110
  average time/residue: 1.0729
  time to fit residues: 122.2273
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  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  292 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain D residue   61 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 33 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   overall best weight:    4.5988

-------------------------------------------------------------------------------
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**
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.099075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.089369 restraints weight = 5611.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.46
r_work: 0.3163 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          1.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4242  Z= 0.267
  Angle     :  0.812   9.323   5670  Z= 0.442
  Chirality :  0.043   0.182    528
  Planarity :  0.004   0.049    804
  Dihedral  :  5.960  16.481    612
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.96 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.75 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP q 334 
 PHE   0.019   0.003   PHE C 289 
 TYR   0.014   0.002   TYR F  45 
 ARG   0.001   0.000   ARG I 293 

*********************** 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
  120 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.432 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8470 (mt0) cc_final: 0.8128 (mt0)
REVERT: A  292 SER cc_start: 0.8931 (t) cc_final: 0.8565 (t)
REVERT: C  292 SER cc_start: 0.9053 (p) cc_final: 0.8808 (p)
REVERT: E  299 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (tp)
  outliers start: 9
  outliers final: 5
  residues processed: 112
  average time/residue: 1.0784
  time to fit residues: 125.1824
Evaluate side-chains
  117 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  292 SER
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain D residue   61 MET
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain E residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0030
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   overall best weight:    1.5994

-------------------------------------------------------------------------------
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**
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.104979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.095188 restraints weight = 5520.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.45
r_work: 0.3245 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          1.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   4242  Z= 0.137
  Angle     :  0.642   7.263   5670  Z= 0.346
  Chirality :  0.038   0.155    528
  Planarity :  0.003   0.047    804
  Dihedral  :  5.327  15.102    612
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 25.26 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.68 (0.18), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.14), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP G 334 
 PHE   0.023   0.002   PHE I 289 
 TYR   0.009   0.001   TYR F  74 
 ARG   0.000   0.000   ARG I 293 

********************** 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
  120 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.397 
Fit side-chains
REVERT: q  303 GLN cc_start: 0.8426 (mt0) cc_final: 0.8109 (mt0)
REVERT: C  292 SER cc_start: 0.9030 (p) cc_final: 0.8706 (p)
REVERT: E  299 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8204 (tp)
REVERT: I  289 PHE cc_start: 0.7359 (t80) cc_final: 0.7146 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 118
  average time/residue: 1.0179
  time to fit residues: 124.6693
Evaluate side-chains
  111 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain E residue  299 LEU
Chi-restraints excluded: chain E residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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  60 ASN
C 303 GLN
** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 327 GLN
H  50 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.099260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.089638 restraints weight = 5571.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.45
r_work: 0.3167 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          1.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4242  Z= 0.272
  Angle     :  0.807   8.917   5670  Z= 0.439
  Chirality :  0.043   0.188    528
  Planarity :  0.004   0.049    804
  Dihedral  :  5.769  15.422    612
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 24.48 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.003   TRP q 334 
 PHE   0.020   0.003   PHE I 289 
 TYR   0.015   0.002   TYR F  45 
 ARG   0.001   0.000   ARG I 293 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4147.88 seconds
wall clock time: 73 minutes 45.64 seconds (4425.64 seconds total)