Starting phenix.real_space_refine
on Sun May  3 07:18:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11nj_75862/05_2026/11nj_75862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11nj_75862/05_2026/11nj_75862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11nj_75862/05_2026/11nj_75862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11nj_75862/05_2026/11nj_75862.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11nj_75862/05_2026/11nj_75862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11nj_75862/05_2026/11nj_75862.map"
  }
  resolution = 2.4
  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=   0.007
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      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    2860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11352
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 207
          Classifications: {'water': 207}
          Link IDs: {None: 206}
    Chain: "B"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 248
          Classifications: {'water': 248}
          Link IDs: {None: 247}
    Chain: "C"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 214
          Classifications: {'water': 214}
          Link IDs: {None: 213}
    Chain: "D"
      Number of atoms: 211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 211
          Classifications: {'water': 211}
          Link IDs: {None: 210}
  Time building chain proxies: 2.76, per 1000 atoms: 0.24
  Number of scatterers: 11352
  At special positions: 0
  Unit cell: (98.49, 81.585, 109.515, 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      44     16.00
     O    2860      8.00
     N    1860      7.00
     C    6588      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: 0.84
  Conformation dependent library (CDL) restraints added in 460.8 milliseconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      53.0% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 4.193A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.932A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 141
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 3.544A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 306 through 314
    Processing helix  chain 'A' and resid 319 through 338
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 45
      removed outlier: 3.849A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 141
    Processing helix  chain 'B' and resid 159 through 180
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 260
      removed outlier: 3.515A  pdb=" N   THR B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 306 through 314
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 338
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 45
      removed outlier: 4.052A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ARG C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.796A  pdb=" N   TYR C  84 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 129 through 139
    Processing helix  chain 'C' and resid 159 through 180
      removed outlier: 3.569A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 260
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 306 through 314
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 338
    Processing helix  chain 'D' and resid 8 through 23
      removed outlier: 3.512A  pdb=" N   VAL D  23 " --> pdb=" O   ALA D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 45
      removed outlier: 4.187A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ARG D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.879A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
      removed outlier: 3.541A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 260
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 306 through 314
    Processing helix  chain 'D' and resid 319 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.870A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   VAL A 267 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   SER A 300 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   PHE A 269 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.784A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ILE B 106 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 5.716A  pdb=" N   GLY C  28 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLY C  75 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE C 144 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   VAL C 267 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   SER C 300 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   PHE C 269 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.834A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA D 145 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLU D 189 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   CYS D 149 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   LEU D 191 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   LEU D 151 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL D 267 " --> pdb=" O   THR D 298 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   SER D 300 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   PHE D 269 " --> pdb=" O   SER D 300 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    548 hydrogen bonds defined for protein.
    1599 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1880
        1.32 -     1.44: 2494
        1.44 -     1.57: 6241
        1.57 -     1.69: 1
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" N   ILE C  46 "
       pdb=" CA  ILE C  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.501 -0.045 1.08e-02 8.57e+03 1.76e+01
  bond pdb=" C   VAL D 260 "
       pdb=" N   PRO D 261 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.18e-02 7.18e+03 1.22e+01
  bond pdb=" N   LYS D 293 "
       pdb=" CA  LYS D 293 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.10e-02 8.26e+03 9.74e+00
  bond pdb=" N   VAL A 264 "
       pdb=" CA  VAL A 264 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.19e-02 7.06e+03 9.69e+00
  bond pdb=" C   PRO A 262 "
       pdb=" O   PRO A 262 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.26e-02 6.30e+03 9.31e+00
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 13884
        1.83 -     3.67: 502
        3.67 -     5.50: 64
        5.50 -     7.34: 13
        7.34 -     9.17: 1
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" N   ALA A 322 "
        pdb=" CA  ALA A 322 "
        pdb=" C   ALA A 322 "
      ideal   model   delta    sigma   weight residual
     111.28  105.90    5.38 1.09e+00 8.42e-01 2.43e+01
  angle pdb=" N   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" C   LYS A 321 "
      ideal   model   delta    sigma   weight residual
     111.36  106.01    5.35 1.09e+00 8.42e-01 2.41e+01
  angle pdb=" CA  PHE D 144 "
        pdb=" CB  PHE D 144 "
        pdb=" CG  PHE D 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.27   -4.47 1.00e+00 1.00e+00 2.00e+01
  angle pdb=" N   ASN B 319 "
        pdb=" CA  ASN B 319 "
        pdb=" C   ASN B 319 "
      ideal   model   delta    sigma   weight residual
     113.02  107.68    5.34 1.20e+00 6.94e-01 1.98e+01
  angle pdb=" C   PRO A 261 "
        pdb=" N   PRO A 262 "
        pdb=" CA  PRO A 262 "
      ideal   model   delta    sigma   weight residual
     119.05  123.99   -4.94 1.11e+00 8.12e-01 1.98e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 6045
       17.74 -    35.47: 341
       35.47 -    53.21: 71
       53.21 -    70.94: 32
       70.94 -    88.68: 15
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  PHE B 299 "
           pdb=" C   PHE B 299 "
           pdb=" N   SER B 300 "
           pdb=" CA  SER B 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.57   16.43     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CB  GLU D 121 "
           pdb=" CG  GLU D 121 "
           pdb=" CD  GLU D 121 "
           pdb=" OE1 GLU D 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.68  -88.68     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CG  ARG C 200 "
           pdb=" CD  ARG C 200 "
           pdb=" NE  ARG C 200 "
           pdb=" CZ  ARG C 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.11  -44.11     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1232
       0.050 -    0.101: 316
       0.101 -    0.151: 71
       0.151 -    0.201: 17
       0.201 -    0.252: 8
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  LEU C  61 "
            pdb=" N   LEU C  61 "
            pdb=" C   LEU C  61 "
            pdb=" CB  LEU C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  ILE C 185 "
            pdb=" N   ILE C 185 "
            pdb=" C   ILE C 185 "
            pdb=" CB  ILE C 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CG  LEU D 320 "
            pdb=" CB  LEU D 320 "
            pdb=" CD1 LEU D 320 "
            pdb=" CD2 LEU D 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 260 "    0.022 2.00e-02 2.50e+03   4.20e-02 1.76e+01
        pdb=" C   VAL D 260 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   VAL D 260 "    0.027 2.00e-02 2.50e+03
        pdb=" N   PRO D 261 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D 326 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.18e+00
        pdb=" C   GLU D 326 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   GLU D 326 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TYR D 327 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 147 "    0.028 2.00e-02 2.50e+03   1.56e-02 6.06e+00
        pdb=" CG  TRP B 147 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 147 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 147 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 147 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 147 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 147 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 147 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 147 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 147 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1577
        2.75 -     3.29: 11450
        3.29 -     3.82: 21312
        3.82 -     4.36: 26923
        4.36 -     4.90: 42218
  Nonbonded interactions: 103480
  Sorted by model distance:
  nonbonded pdb=" O   GLN D  60 "
            pdb=" OG1 THR D  64 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   GLN C  60 "
            pdb=" OG1 THR C  64 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OH  TYR B  84 "
            pdb=" OD2 ASP B 140 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   HOH A 435 "
            pdb=" O   HOH A 554 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   ALA C  87 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.312 3.040
  ... (remaining 103475 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             5.750
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.870
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  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:8.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
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      :  0.007   0.095  10672  Z= 0.348
  Angle     :  0.786   9.170  14464  Z= 0.487
  Chirality :  0.051   0.252   1644
  Planarity :  0.007   0.059   1880
  Dihedral  : 13.300  88.679   3984
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  0.63 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.63 (0.23), residues: 1364
  helix:  1.38 (0.19), residues: 712
  sheet: -1.19 (0.35), residues: 220
  loop : -0.12 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 172 
 TYR   0.021   0.002   TYR D 213 
 PHE   0.023   0.003   PHE D 144 
 TRP   0.037   0.005   TRP A 147 
 HIS   0.013   0.003   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 (10672)
  covalent geometry    : angle       0.78578 (14464)
  hydrogen bonds       : bond        0.14957 (  548)
  hydrogen bonds       : angle       5.75937 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.7808 (ptpp) cc_final: 0.7030 (mmtm)
REVERT: A  152 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7393 (pttm)
REVERT: A  165 GLU cc_start: 0.8039 (tp30) cc_final: 0.7830 (tp30)
REVERT: B   49 GLU cc_start: 0.7698 (pm20) cc_final: 0.7491 (pt0)
REVERT: B   66 ASP cc_start: 0.7925 (t70) cc_final: 0.7464 (t70)
REVERT: B  199 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7382 (ttpp)
REVERT: B  303 ARG cc_start: 0.8052 (ttm110) cc_final: 0.6837 (tpp-160)
REVERT: C   53 GLU cc_start: 0.7949 (tp30) cc_final: 0.7489 (tp30)
REVERT: C   86 LYS cc_start: 0.7999 (mttt) cc_final: 0.7306 (mtmt)
REVERT: C  132 GLU cc_start: 0.8206 (mp0) cc_final: 0.7740 (mp0)
REVERT: C  237 HIS cc_start: 0.7831 (t70) cc_final: 0.7141 (m170)
REVERT: C  242 LYS cc_start: 0.7919 (mttm) cc_final: 0.7564 (tptt)
REVERT: C  303 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.6295 (ttt90)
REVERT: C  341 LYS cc_start: 0.8298 (mttt) cc_final: 0.8068 (mtpt)
REVERT: D   41 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7466 (mttm)
REVERT: D   86 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7785 (mttm)
REVERT: D  288 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8075 (mtmt)
  outliers start: 15
  outliers final: 6
  residues processed: 187
  average time/residue: 0.9144
  time to fit residues: 179.8808
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A   4 HIS
B 119 ASN
B 241 GLN
B 306 GLN
B 334 ASN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 324 GLN
D  95 GLN
D 119 ASN
D 231 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109765 restraints weight = 11871.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.51
r_work: 0.3227 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10672  Z= 0.119
  Angle     :  0.514   9.525  14464  Z= 0.268
  Chirality :  0.041   0.149   1644
  Planarity :  0.004   0.046   1880
  Dihedral  :  5.318  59.997   1485
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  8.09 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.40 (0.23), residues: 1364
  helix:  2.19 (0.19), residues: 712
  sheet: -1.72 (0.34), residues: 204
  loop :  0.33 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 330 
 TYR   0.020   0.002   TYR D 213 
 PHE   0.011   0.001   PHE C 144 
 TRP   0.014   0.002   TRP D 147 
 HIS   0.004   0.001   HIS B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10672)
  covalent geometry    : angle       0.51395 (14464)
  hydrogen bonds       : bond        0.04870 (  548)
  hydrogen bonds       : angle       4.17465 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.7820 (ptpp) cc_final: 0.7116 (mmtm)
REVERT: A  152 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7460 (pttm)
REVERT: A  295 TRP cc_start: 0.8823 (OUTLIER) cc_final: 0.7729 (m-90)
REVERT: B   41 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6766 (mptp)
REVERT: B   66 ASP cc_start: 0.7623 (t70) cc_final: 0.7118 (m-30)
REVERT: B  199 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7770 (ttpp)
REVERT: B  303 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7067 (ttt-90)
REVERT: B  317 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7468 (tptm)
REVERT: C   52 GLU cc_start: 0.8130 (tt0) cc_final: 0.7766 (tt0)
REVERT: C   81 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7681 (tt0)
REVERT: C   86 LYS cc_start: 0.8195 (mttt) cc_final: 0.7571 (mtmt)
REVERT: C  132 GLU cc_start: 0.8332 (mp0) cc_final: 0.7828 (mp0)
REVERT: C  155 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6634 (tt0)
REVERT: C  237 HIS cc_start: 0.7903 (t70) cc_final: 0.7487 (m170)
REVERT: C  303 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.6827 (ttt-90)
REVERT: D   41 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7688 (mptt)
REVERT: D   49 GLU cc_start: 0.6776 (pm20) cc_final: 0.6544 (pm20)
REVERT: D   52 GLU cc_start: 0.7570 (tp30) cc_final: 0.7238 (tt0)
REVERT: D   86 LYS cc_start: 0.8263 (mtmm) cc_final: 0.8001 (mttt)
REVERT: D  206 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8309 (mt-10)
REVERT: D  234 THR cc_start: 0.8485 (m) cc_final: 0.8087 (p)
REVERT: D  241 GLN cc_start: 0.7697 (tt0) cc_final: 0.7345 (tp40)
REVERT: D  278 GLU cc_start: 0.8071 (tt0) cc_final: 0.7832 (tt0)
REVERT: D  288 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8240 (mtmt)
  outliers start: 26
  outliers final: 10
  residues processed: 133
  average time/residue: 0.9189
  time to fit residues: 128.8046
Evaluate side-chains
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 58 optimal weight:    0.0870
   chunk 77 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 127 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
B   4 HIS
B  95 GLN
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  54 ASN
C 168 ASN
C 219 HIS
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.111009 restraints weight = 12035.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.52
r_work: 0.3250 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10672  Z= 0.098
  Angle     :  0.458   7.744  14464  Z= 0.237
  Chirality :  0.039   0.136   1644
  Planarity :  0.004   0.036   1880
  Dihedral  :  5.035  59.725   1485
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  8.90 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.73 (0.24), residues: 1364
  helix:  2.51 (0.19), residues: 712
  sheet: -1.71 (0.34), residues: 204
  loop :  0.44 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 303 
 TYR   0.016   0.001   TYR D 213 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.011   0.001   TRP C 147 
 HIS   0.003   0.001   HIS B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10672)
  covalent geometry    : angle       0.45816 (14464)
  hydrogen bonds       : bond        0.04130 (  548)
  hydrogen bonds       : angle       3.84365 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7310 (tt0)
REVERT: A  139 LYS cc_start: 0.7755 (ptpp) cc_final: 0.7084 (mmtm)
REVERT: A  152 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7621 (pttm)
REVERT: A  295 TRP cc_start: 0.8848 (OUTLIER) cc_final: 0.7687 (m-90)
REVERT: A  317 LYS cc_start: 0.6714 (ttpp) cc_final: 0.6334 (mmtm)
REVERT: A  321 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6265 (tttt)
REVERT: B   41 LYS cc_start: 0.7426 (mppt) cc_final: 0.6830 (mptp)
REVERT: B   66 ASP cc_start: 0.7575 (t70) cc_final: 0.7102 (m-30)
REVERT: B  139 LYS cc_start: 0.7828 (ptpp) cc_final: 0.7222 (tttm)
REVERT: B  199 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7709 (ttpp)
REVERT: B  303 ARG cc_start: 0.8236 (ttm110) cc_final: 0.6951 (ttt-90)
REVERT: B  317 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7411 (tptm)
REVERT: B  321 LYS cc_start: 0.8139 (tppt) cc_final: 0.7838 (mmtt)
REVERT: C   86 LYS cc_start: 0.8187 (mttt) cc_final: 0.7573 (mtmt)
REVERT: C  132 GLU cc_start: 0.8301 (mp0) cc_final: 0.7780 (mp0)
REVERT: C  155 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6694 (tt0)
REVERT: C  237 HIS cc_start: 0.7886 (t70) cc_final: 0.7510 (m170)
REVERT: C  292 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7947 (tt)
REVERT: C  303 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.6807 (ttt-90)
REVERT: D   41 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7692 (mptt)
REVERT: D   49 GLU cc_start: 0.6784 (pm20) cc_final: 0.6578 (pm20)
REVERT: D   86 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7969 (mttt)
REVERT: D  206 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: D  234 THR cc_start: 0.8478 (m) cc_final: 0.8080 (p)
REVERT: D  237 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6869 (t-170)
REVERT: D  241 GLN cc_start: 0.7732 (tt0) cc_final: 0.7344 (tp40)
REVERT: D  278 GLU cc_start: 0.8066 (tt0) cc_final: 0.7865 (tt0)
  outliers start: 25
  outliers final: 7
  residues processed: 120
  average time/residue: 0.9755
  time to fit residues: 123.2177
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  237 HIS
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 114 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.136391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.106022 restraints weight = 11990.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.54
r_work: 0.3163 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10672  Z= 0.127
  Angle     :  0.495   6.390  14464  Z= 0.259
  Chirality :  0.041   0.154   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  4.912  57.476   1480
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  9.08 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.67 (0.23), residues: 1364
  helix:  2.52 (0.19), residues: 712
  sheet: -1.80 (0.34), residues: 204
  loop :  0.35 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.022   0.002   TYR D 213 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.016   0.002   TRP D 147 
 HIS   0.005   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10672)
  covalent geometry    : angle       0.49521 (14464)
  hydrogen bonds       : bond        0.04956 (  548)
  hydrogen bonds       : angle       3.90379 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7233 (tt0)
REVERT: A  139 LYS cc_start: 0.7845 (ptpp) cc_final: 0.6942 (mmtm)
REVERT: A  152 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7450 (pttm)
REVERT: A  317 LYS cc_start: 0.6723 (ttpp) cc_final: 0.6299 (mmtm)
REVERT: B   41 LYS cc_start: 0.7259 (mppt) cc_final: 0.6633 (mptp)
REVERT: B   66 ASP cc_start: 0.7642 (t70) cc_final: 0.7072 (m-30)
REVERT: B  139 LYS cc_start: 0.7762 (ptpp) cc_final: 0.7080 (tttm)
REVERT: B  199 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7636 (ttpp)
REVERT: B  303 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7379 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7403 (tptm)
REVERT: B  321 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7740 (mmtt)
REVERT: C   52 GLU cc_start: 0.8005 (tt0) cc_final: 0.7584 (tt0)
REVERT: C   67 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6172 (t0)
REVERT: C   86 LYS cc_start: 0.8124 (mttt) cc_final: 0.7469 (mtmt)
REVERT: C  132 GLU cc_start: 0.8324 (mp0) cc_final: 0.7684 (mp0)
REVERT: C  155 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6577 (tt0)
REVERT: C  173 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8362 (t80)
REVERT: C  189 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8349 (tt0)
REVERT: C  237 HIS cc_start: 0.7882 (t70) cc_final: 0.7326 (m170)
REVERT: C  292 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7908 (tt)
REVERT: C  297 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8701 (mm)
REVERT: C  303 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.6721 (ttt-90)
REVERT: D   41 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7657 (mptt)
REVERT: D   49 GLU cc_start: 0.6714 (pm20) cc_final: 0.6459 (pm20)
REVERT: D   86 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7800 (mttt)
REVERT: D  155 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7132 (tp30)
REVERT: D  173 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.7939 (t80)
REVERT: D  206 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8343 (mt-10)
REVERT: D  234 THR cc_start: 0.8481 (m) cc_final: 0.7994 (p)
  outliers start: 25
  outliers final: 10
  residues processed: 116
  average time/residue: 0.9301
  time to fit residues: 113.9650
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  189 GLU
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN
B  95 GLN
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D   4 HIS
D  95 GLN
D 219 HIS
D 284 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.133961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.103541 restraints weight = 11890.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.54
r_work: 0.3134 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10672  Z= 0.160
  Angle     :  0.534   6.407  14464  Z= 0.280
  Chirality :  0.043   0.161   1644
  Planarity :  0.004   0.037   1880
  Dihedral  :  5.157  54.265   1480
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.08 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.56 (0.23), residues: 1364
  helix:  2.39 (0.19), residues: 712
  sheet: -1.60 (0.36), residues: 184
  loop :  0.12 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 133 
 TYR   0.024   0.002   TYR C 213 
 PHE   0.019   0.002   PHE B 144 
 TRP   0.016   0.002   TRP D 147 
 HIS   0.005   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10672)
  covalent geometry    : angle       0.53428 (14464)
  hydrogen bonds       : bond        0.05615 (  548)
  hydrogen bonds       : angle       4.03155 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8038 (tt0)
REVERT: A   81 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7278 (tt0)
REVERT: A  139 LYS cc_start: 0.8101 (ptpp) cc_final: 0.6992 (mmtm)
REVERT: A  152 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7465 (pttm)
REVERT: A  317 LYS cc_start: 0.6777 (ttpp) cc_final: 0.6368 (mmtm)
REVERT: B   41 LYS cc_start: 0.7271 (mppt) cc_final: 0.6681 (mptp)
REVERT: B   66 ASP cc_start: 0.7671 (t70) cc_final: 0.7210 (m-30)
REVERT: B  199 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7699 (ttpp)
REVERT: B  303 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7377 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7442 (tptm)
REVERT: B  321 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7865 (mmtt)
REVERT: C   52 GLU cc_start: 0.8020 (tt0) cc_final: 0.7598 (tt0)
REVERT: C   67 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6109 (t0)
REVERT: C   86 LYS cc_start: 0.8099 (mttt) cc_final: 0.7367 (mtmm)
REVERT: C  132 GLU cc_start: 0.8382 (mp0) cc_final: 0.7788 (mp0)
REVERT: C  155 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6691 (tt0)
REVERT: C  173 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8448 (t80)
REVERT: C  237 HIS cc_start: 0.7889 (t70) cc_final: 0.7278 (m170)
REVERT: C  292 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7931 (tt)
REVERT: C  303 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.6728 (ttt-90)
REVERT: D   41 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7641 (mptt)
REVERT: D   86 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7816 (mttt)
REVERT: D  155 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7103 (tp30)
REVERT: D  173 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.7959 (t80)
REVERT: D  206 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8363 (mt-10)
REVERT: D  234 THR cc_start: 0.8556 (m) cc_final: 0.8065 (p)
  outliers start: 28
  outliers final: 12
  residues processed: 116
  average time/residue: 0.9276
  time to fit residues: 113.5833
Evaluate side-chains
  110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   chunk 122 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 58 optimal weight:    0.1980
   chunk 101 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 80 optimal weight:    8.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
B  95 GLN
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN
D 136 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.137626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.108174 restraints weight = 12010.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.51
r_work: 0.3207 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10672  Z= 0.103
  Angle     :  0.456   5.777  14464  Z= 0.238
  Chirality :  0.039   0.142   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  4.836  54.999   1480
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  9.08 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.78 (0.23), residues: 1364
  helix:  2.62 (0.19), residues: 712
  sheet: -1.60 (0.35), residues: 184
  loop :  0.19 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  59 
 TYR   0.015   0.001   TYR D 213 
 PHE   0.014   0.001   PHE B 144 
 TRP   0.012   0.001   TRP D 147 
 HIS   0.002   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (10672)
  covalent geometry    : angle       0.45626 (14464)
  hydrogen bonds       : bond        0.04284 (  548)
  hydrogen bonds       : angle       3.80983 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7318 (tt0)
REVERT: A  152 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7694 (pttm)
REVERT: A  317 LYS cc_start: 0.6872 (ttpp) cc_final: 0.6520 (mmtp)
REVERT: A  321 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6388 (tttt)
REVERT: B   41 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6937 (mptp)
REVERT: B   66 ASP cc_start: 0.7579 (t70) cc_final: 0.7218 (m-30)
REVERT: B  139 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7178 (tttm)
REVERT: B  199 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7776 (ttpp)
REVERT: B  303 ARG cc_start: 0.8269 (ttm110) cc_final: 0.7538 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7486 (tptm)
REVERT: B  321 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7885 (mmtt)
REVERT: C   52 GLU cc_start: 0.8079 (tt0) cc_final: 0.7678 (tt0)
REVERT: C   67 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6314 (t0)
REVERT: C   86 LYS cc_start: 0.8231 (mttt) cc_final: 0.7640 (mtmt)
REVERT: C  132 GLU cc_start: 0.8364 (mp0) cc_final: 0.7806 (mp0)
REVERT: C  139 LYS cc_start: 0.8403 (ptpp) cc_final: 0.7714 (pttp)
REVERT: C  155 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6708 (tt0)
REVERT: C  173 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8279 (t80)
REVERT: C  237 HIS cc_start: 0.7903 (t70) cc_final: 0.7450 (m170)
REVERT: C  292 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7990 (tt)
REVERT: C  303 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.6981 (ttt-90)
REVERT: D   41 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7751 (mptt)
REVERT: D   49 GLU cc_start: 0.6786 (pt0) cc_final: 0.6225 (pm20)
REVERT: D   86 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7943 (mttt)
REVERT: D  155 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7182 (tp30)
REVERT: D  173 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.7815 (t80)
REVERT: D  206 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8332 (mt-10)
REVERT: D  234 THR cc_start: 0.8595 (m) cc_final: 0.8188 (p)
REVERT: D  320 LEU cc_start: 0.6939 (pp) cc_final: 0.6511 (tt)
  outliers start: 29
  outliers final: 9
  residues processed: 117
  average time/residue: 0.9233
  time to fit residues: 114.0837
Evaluate side-chains
  110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 118 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105173 restraints weight = 11948.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.54
r_work: 0.3148 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10672  Z= 0.130
  Angle     :  0.493   6.774  14464  Z= 0.258
  Chirality :  0.041   0.154   1644
  Planarity :  0.004   0.036   1880
  Dihedral  :  4.972  53.953   1480
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  9.53 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.68 (0.23), residues: 1364
  helix:  2.55 (0.19), residues: 712
  sheet: -1.72 (0.35), residues: 176
  loop :  0.11 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 258 
 TYR   0.021   0.002   TYR C 213 
 PHE   0.016   0.001   PHE B 144 
 TRP   0.014   0.002   TRP A 147 
 HIS   0.003   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10672)
  covalent geometry    : angle       0.49335 (14464)
  hydrogen bonds       : bond        0.04951 (  548)
  hydrogen bonds       : angle       3.88353 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7276 (tt0)
REVERT: A  152 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7456 (pttm)
REVERT: A  311 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7095 (mtpt)
REVERT: A  317 LYS cc_start: 0.6777 (ttpp) cc_final: 0.6406 (mmtp)
REVERT: A  321 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6499 (mmmt)
REVERT: B   41 LYS cc_start: 0.7264 (mppt) cc_final: 0.6672 (mptp)
REVERT: B   49 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7505 (pt0)
REVERT: B   66 ASP cc_start: 0.7627 (t70) cc_final: 0.7181 (m-30)
REVERT: B  139 LYS cc_start: 0.7814 (ptpp) cc_final: 0.7096 (tttm)
REVERT: B  199 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7663 (ttpp)
REVERT: B  303 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7340 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7395 (tptm)
REVERT: B  321 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7836 (mmtt)
REVERT: C   67 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6044 (t0)
REVERT: C   86 LYS cc_start: 0.8058 (mttt) cc_final: 0.7440 (mtmt)
REVERT: C  132 GLU cc_start: 0.8358 (mp0) cc_final: 0.7745 (mp0)
REVERT: C  155 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6605 (tt0)
REVERT: C  173 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8351 (t80)
REVERT: C  237 HIS cc_start: 0.7870 (t70) cc_final: 0.7278 (m170)
REVERT: C  292 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7952 (tt)
REVERT: C  303 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.6773 (ttt-90)
REVERT: D   41 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7615 (mptt)
REVERT: D   86 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7759 (mttt)
REVERT: D  139 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7790 (ptpt)
REVERT: D  155 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7104 (tp30)
REVERT: D  173 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.7941 (t80)
REVERT: D  206 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8339 (mt-10)
REVERT: D  320 LEU cc_start: 0.6836 (pp) cc_final: 0.6426 (tt)
  outliers start: 27
  outliers final: 11
  residues processed: 107
  average time/residue: 0.9194
  time to fit residues: 103.8925
Evaluate side-chains
  112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 134 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0670
   chunk 30 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7518

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.137229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.107775 restraints weight = 11980.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.50
r_work: 0.3216 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10672  Z= 0.106
  Angle     :  0.462   7.137  14464  Z= 0.240
  Chirality :  0.039   0.138   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  4.826  54.126   1480
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  9.62 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.72 (0.23), residues: 1364
  helix:  2.57 (0.19), residues: 720
  sheet: -1.70 (0.35), residues: 176
  loop :  0.09 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  59 
 TYR   0.016   0.001   TYR D 213 
 PHE   0.014   0.001   PHE B 144 
 TRP   0.011   0.001   TRP D 147 
 HIS   0.002   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10672)
  covalent geometry    : angle       0.46249 (14464)
  hydrogen bonds       : bond        0.04339 (  548)
  hydrogen bonds       : angle       3.78333 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   73 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7906 (mp)
REVERT: A   81 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7279 (tt0)
REVERT: A  152 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7598 (pttm)
REVERT: A  311 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7096 (mtpt)
REVERT: A  317 LYS cc_start: 0.6752 (ttpp) cc_final: 0.6416 (mmtp)
REVERT: A  321 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6505 (mmmt)
REVERT: B   41 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6857 (mptp)
REVERT: B   49 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7529 (pt0)
REVERT: B   66 ASP cc_start: 0.7547 (t70) cc_final: 0.7159 (m-30)
REVERT: B  139 LYS cc_start: 0.7798 (ptpp) cc_final: 0.7126 (tttm)
REVERT: B  199 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7690 (ttpp)
REVERT: B  303 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7445 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7402 (tptm)
REVERT: B  321 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7837 (mmtt)
REVERT: C   67 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6158 (t0)
REVERT: C   86 LYS cc_start: 0.8139 (mttt) cc_final: 0.7559 (mtmt)
REVERT: C  132 GLU cc_start: 0.8345 (mp0) cc_final: 0.7755 (mp0)
REVERT: C  139 LYS cc_start: 0.8374 (ptpp) cc_final: 0.7690 (pttp)
REVERT: C  155 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6657 (tt0)
REVERT: C  173 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8251 (t80)
REVERT: C  237 HIS cc_start: 0.7883 (t70) cc_final: 0.7377 (m170)
REVERT: C  292 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7976 (tt)
REVERT: C  303 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.6885 (ttt-90)
REVERT: D   41 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7679 (mptt)
REVERT: D   49 GLU cc_start: 0.6891 (pt0) cc_final: 0.6203 (pm20)
REVERT: D   86 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7849 (mttt)
REVERT: D  155 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7197 (tp30)
REVERT: D  173 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.7890 (t80)
REVERT: D  206 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8343 (mt-10)
REVERT: D  234 THR cc_start: 0.8516 (m) cc_final: 0.8111 (p)
REVERT: D  288 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8210 (mtmm)
REVERT: D  320 LEU cc_start: 0.6905 (pp) cc_final: 0.6576 (tt)
  outliers start: 27
  outliers final: 10
  residues processed: 108
  average time/residue: 0.9306
  time to fit residues: 106.1056
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  288 LYS
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 121 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 94 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.135748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.105571 restraints weight = 11869.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.54
r_work: 0.3137 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10672  Z= 0.127
  Angle     :  0.488   5.889  14464  Z= 0.254
  Chirality :  0.040   0.146   1644
  Planarity :  0.004   0.036   1880
  Dihedral  :  4.947  53.291   1480
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.89 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.64 (0.23), residues: 1364
  helix:  2.50 (0.19), residues: 720
  sheet: -1.70 (0.35), residues: 176
  loop :  0.07 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 258 
 TYR   0.020   0.002   TYR D 213 
 PHE   0.017   0.001   PHE B 144 
 TRP   0.013   0.002   TRP D 147 
 HIS   0.003   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10672)
  covalent geometry    : angle       0.48792 (14464)
  hydrogen bonds       : bond        0.04856 (  548)
  hydrogen bonds       : angle       3.85027 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   73 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7817 (mp)
REVERT: A   81 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7283 (tt0)
REVERT: A  152 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7469 (pttm)
REVERT: A  317 LYS cc_start: 0.6717 (ttpp) cc_final: 0.6373 (mmtp)
REVERT: A  321 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6487 (mmmt)
REVERT: B   41 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6683 (mptp)
REVERT: B   49 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7612 (pt0)
REVERT: B   66 ASP cc_start: 0.7594 (t70) cc_final: 0.7166 (m-30)
REVERT: B  139 LYS cc_start: 0.7796 (ptpp) cc_final: 0.7088 (tttm)
REVERT: B  199 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7662 (ttpp)
REVERT: B  303 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7357 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7343 (tptm)
REVERT: B  321 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7828 (mmtt)
REVERT: C   67 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6033 (t0)
REVERT: C   86 LYS cc_start: 0.8054 (mttt) cc_final: 0.7457 (mtmt)
REVERT: C  132 GLU cc_start: 0.8361 (mp0) cc_final: 0.7752 (mp0)
REVERT: C  139 LYS cc_start: 0.8373 (ptpp) cc_final: 0.7616 (pttp)
REVERT: C  155 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6607 (tt0)
REVERT: C  173 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8335 (t80)
REVERT: C  237 HIS cc_start: 0.7859 (t70) cc_final: 0.7266 (m170)
REVERT: C  292 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7981 (tt)
REVERT: C  303 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.6769 (ttt-90)
REVERT: D   41 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7607 (mptt)
REVERT: D   86 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7755 (mttt)
REVERT: D  155 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7206 (tp30)
REVERT: D  173 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.7905 (t80)
REVERT: D  206 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8340 (mt-10)
REVERT: D  320 LEU cc_start: 0.6830 (pp) cc_final: 0.6534 (tt)
  outliers start: 24
  outliers final: 11
  residues processed: 107
  average time/residue: 0.9164
  time to fit residues: 103.4218
Evaluate side-chains
  111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0050
   chunk 43 optimal weight:    0.0000
   chunk 100 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0970
   chunk 129 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.138372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.109067 restraints weight = 12013.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.51
r_work: 0.3227 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10672  Z= 0.097
  Angle     :  0.445   5.607  14464  Z= 0.231
  Chirality :  0.039   0.128   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  4.725  53.712   1480
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.07 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.80 (0.23), residues: 1364
  helix:  2.65 (0.19), residues: 720
  sheet: -1.72 (0.35), residues: 176
  loop :  0.13 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  59 
 TYR   0.014   0.001   TYR D 213 
 PHE   0.013   0.001   PHE B 144 
 TRP   0.010   0.001   TRP D 147 
 HIS   0.002   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (10672)
  covalent geometry    : angle       0.44526 (14464)
  hydrogen bonds       : bond        0.04026 (  548)
  hydrogen bonds       : angle       3.71009 ( 1599)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   73 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7861 (mp)
REVERT: A   81 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7291 (tt0)
REVERT: A  152 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7542 (pttm)
REVERT: A  311 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7077 (mtpt)
REVERT: A  317 LYS cc_start: 0.6646 (ttpp) cc_final: 0.6376 (mmtp)
REVERT: A  321 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6534 (mmmt)
REVERT: B   41 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6835 (mptp)
REVERT: B   49 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7631 (pt0)
REVERT: B   66 ASP cc_start: 0.7537 (t70) cc_final: 0.7125 (m-30)
REVERT: B  139 LYS cc_start: 0.7796 (ptpp) cc_final: 0.7154 (tttm)
REVERT: B  199 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7628 (ttpp)
REVERT: B  303 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7342 (tpp-160)
REVERT: B  317 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7348 (tptm)
REVERT: B  321 LYS cc_start: 0.8123 (tppt) cc_final: 0.7829 (mmtt)
REVERT: C   67 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6130 (t0)
REVERT: C   86 LYS cc_start: 0.8092 (mttt) cc_final: 0.7490 (mtmt)
REVERT: C  132 GLU cc_start: 0.8325 (mp0) cc_final: 0.7732 (mp0)
REVERT: C  139 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7651 (pttp)
REVERT: C  155 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6613 (tt0)
REVERT: C  173 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8152 (t80)
REVERT: C  237 HIS cc_start: 0.7853 (t70) cc_final: 0.7382 (m170)
REVERT: C  292 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7976 (tt)
REVERT: C  303 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.6856 (ttt-90)
REVERT: D   41 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7651 (mptt)
REVERT: D   49 GLU cc_start: 0.6939 (pt0) cc_final: 0.6201 (pm20)
REVERT: D   86 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7826 (mttt)
REVERT: D  155 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7198 (tp30)
REVERT: D  173 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7783 (t80)
REVERT: D  206 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: D  320 LEU cc_start: 0.6853 (pp) cc_final: 0.6611 (tt)
  outliers start: 23
  outliers final: 9
  residues processed: 110
  average time/residue: 0.9491
  time to fit residues: 109.8653
Evaluate side-chains
  110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
B 241 GLN
** C  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 GLN
D  95 GLN
D 136 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.137126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.106956 restraints weight = 11983.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.55
r_work: 0.3167 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10672  Z= 0.112
  Angle     :  0.469   7.344  14464  Z= 0.243
  Chirality :  0.040   0.135   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  4.815  53.246   1480
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.25 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.76 (0.23), residues: 1364
  helix:  2.62 (0.19), residues: 720
  sheet: -1.69 (0.35), residues: 176
  loop :  0.09 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 258 
 TYR   0.018   0.001   TYR D 213 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.012   0.001   TRP D 147 
 HIS   0.002   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10672)
  covalent geometry    : angle       0.46893 (14464)
  hydrogen bonds       : bond        0.04444 (  548)
  hydrogen bonds       : angle       3.76056 ( 1599)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4271.84 seconds
wall clock time: 73 minutes 41.68 seconds (4421.68 seconds total)