Starting phenix.real_space_refine
on Thu Sep 18 00:47:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngr_49391/09_2025/9ngr_49391_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngr_49391/09_2025/9ngr_49391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ngr_49391/09_2025/9ngr_49391_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngr_49391/09_2025/9ngr_49391_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngr_49391/09_2025/9ngr_49391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngr_49391/09_2025/9ngr_49391.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     Na      6      4.78       5
     C    8180      2.51       5
     N    2085      2.21       5
     O    2250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12551
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "B"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "C"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "D"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "E"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 7
          Unusual residues: {' NA': 3, '3CN': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 7
          Unusual residues: {' NA': 3, '3CN': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.53, per 1000 atoms: 0.20
  Number of scatterers: 12551
  At special positions: 0
  Unit cell: (89.96, 89.095, 123.695, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     Na      6     11.00
     O    2250      8.00
     N    2085      7.00
     C    8180      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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 609.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 15 sheets defined
      34.2% alpha, 35.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 4.139A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 227 through 251
      removed outlier: 3.600A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASN A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 285
    Processing helix  chain 'A' and resid 303 through 317
      removed outlier: 3.596A  pdb=" N   ILE A 317 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 4.139A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 179
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 227 through 251
      removed outlier: 3.600A  pdb=" N   ARG B 231 " --> pdb=" O   SER B 227 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 250 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASN B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 285
    Processing helix  chain 'B' and resid 303 through 317
      removed outlier: 3.596A  pdb=" N   ILE B 317 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 4.139A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 179
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 227 through 251
      removed outlier: 3.600A  pdb=" N   ARG C 231 " --> pdb=" O   SER C 227 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER C 250 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASN C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 285
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 3.595A  pdb=" N   ILE C 317 " --> pdb=" O   CYS C 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 4.139A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 179
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 227 through 251
      removed outlier: 3.600A  pdb=" N   ARG D 231 " --> pdb=" O   SER D 227 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASN D 251 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 285
    Processing helix  chain 'D' and resid 303 through 317
      removed outlier: 3.596A  pdb=" N   ILE D 317 " --> pdb=" O   CYS D 313 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 4.140A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 179
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
    Processing helix  chain 'E' and resid 222 through 225
    Processing helix  chain 'E' and resid 227 through 251
      removed outlier: 3.599A  pdb=" N   ARG E 231 " --> pdb=" O   SER E 227 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER E 250 " --> pdb=" O   ALA E 246 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASN E 251 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 285
    Processing helix  chain 'E' and resid 303 through 317
      removed outlier: 3.595A  pdb=" N   ILE E 317 " --> pdb=" O   CYS E 313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 27
      removed outlier: 6.868A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A  37 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.512A  pdb=" N   GLY A  37 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   VAL A  16 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE A 188 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   SER A 171 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG A 190 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   HIS A 169 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   THR A 192 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER A 167 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ARG A 194 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS A 165 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ASP A 196 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 27
      removed outlier: 6.868A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.512A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE B 188 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   SER B 171 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG B 190 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   HIS B 169 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   THR B 192 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER B 167 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS B 165 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ASP B 196 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 27
      removed outlier: 6.867A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY C  37 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 82
      removed outlier: 4.124A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY C  37 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE C 188 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   SER C 171 " --> pdb=" O   PHE C 188 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG C 190 " --> pdb=" O   HIS C 169 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   HIS C 169 " --> pdb=" O   ARG C 190 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   THR C 192 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER C 167 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ARG C 194 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS C 165 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ASP C 196 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 27
      removed outlier: 6.868A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.511A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   VAL D  16 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE D 188 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   SER D 171 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG D 190 " --> pdb=" O   HIS D 169 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   HIS D 169 " --> pdb=" O   ARG D 190 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   THR D 192 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER D 167 " --> pdb=" O   THR D 192 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ARG D 194 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS D 165 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ASP D 196 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 27
      removed outlier: 6.868A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY E  37 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.511A  pdb=" N   GLY E  37 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   VAL E  16 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.572A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   PHE E 188 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   SER E 171 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ARG E 190 " --> pdb=" O   HIS E 169 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   HIS E 169 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   THR E 192 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER E 167 " --> pdb=" O   THR E 192 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ARG E 194 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS E 165 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ASP E 196 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)

    601 hydrogen bonds defined for protein.
    1731 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3983
        1.34 -     1.46: 2606
        1.46 -     1.57: 6241
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" N   ILE E 252 "
       pdb=" CA  ILE E 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.038 9.10e-03 1.21e+04 1.72e+01
  bond pdb=" N   ILE B 252 "
       pdb=" CA  ILE B 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 9.10e-03 1.21e+04 1.66e+01
  bond pdb=" N   ILE A 252 "
       pdb=" CA  ILE A 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 9.10e-03 1.21e+04 1.65e+01
  bond pdb=" N   ILE D 252 "
       pdb=" CA  ILE D 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 9.10e-03 1.21e+04 1.64e+01
  bond pdb=" N   ILE C 252 "
       pdb=" CA  ILE C 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 9.10e-03 1.21e+04 1.61e+01
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 16226
        1.46 -     2.92: 1039
        2.92 -     4.37: 200
        4.37 -     5.83: 60
        5.83 -     7.29: 20
  Bond angle restraints: 17545
  Sorted by residual:
  angle pdb=" C   ASN B 251 "
        pdb=" N   ILE B 252 "
        pdb=" CA  ILE B 252 "
      ideal   model   delta    sigma   weight residual
     122.14  118.14    4.00 1.11e+00 8.12e-01 1.30e+01
  angle pdb=" CA  THR D 237 "
        pdb=" CB  THR D 237 "
        pdb=" OG1 THR D 237 "
      ideal   model   delta    sigma   weight residual
     109.60  104.23    5.37 1.50e+00 4.44e-01 1.28e+01
  angle pdb=" C   ASN D 251 "
        pdb=" N   ILE D 252 "
        pdb=" CA  ILE D 252 "
      ideal   model   delta    sigma   weight residual
     122.14  118.19    3.95 1.11e+00 8.12e-01 1.27e+01
  angle pdb=" CA  THR C 237 "
        pdb=" CB  THR C 237 "
        pdb=" OG1 THR C 237 "
      ideal   model   delta    sigma   weight residual
     109.60  104.27    5.33 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" CA  ASP A 158 "
        pdb=" CB  ASP A 158 "
        pdb=" CG  ASP A 158 "
      ideal   model   delta    sigma   weight residual
     112.60  116.15   -3.55 1.00e+00 1.00e+00 1.26e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6785
       17.91 -    35.83: 614
       35.83 -    53.74: 96
       53.74 -    71.65: 30
       71.65 -    89.57: 5
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  SER B 227 "
           pdb=" C   SER B 227 "
           pdb=" N   PHE B 228 "
           pdb=" CA  PHE B 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.00  -24.00     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  SER C 227 "
           pdb=" C   SER C 227 "
           pdb=" N   PHE C 228 "
           pdb=" CA  PHE C 228 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.02  -23.98     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  SER D 227 "
           pdb=" C   SER D 227 "
           pdb=" N   PHE D 228 "
           pdb=" CA  PHE D 228 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.03  -23.97     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1178
       0.041 -    0.082: 449
       0.082 -    0.123: 247
       0.123 -    0.165: 59
       0.165 -    0.206: 17
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CA  ILE C 157 "
            pdb=" N   ILE C 157 "
            pdb=" C   ILE C 157 "
            pdb=" CB  ILE C 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE E 157 "
            pdb=" N   ILE E 157 "
            pdb=" C   ILE E 157 "
            pdb=" CB  ILE E 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ILE A 157 "
            pdb=" N   ILE A 157 "
            pdb=" C   ILE A 157 "
            pdb=" CB  ILE A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 210 "   -0.042 5.00e-02 4.00e+02   6.35e-02 6.45e+00
        pdb=" N   PRO B 211 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 211 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 211 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 210 "    0.042 5.00e-02 4.00e+02   6.35e-02 6.44e+00
        pdb=" N   PRO E 211 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO E 211 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 211 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 210 "    0.042 5.00e-02 4.00e+02   6.34e-02 6.42e+00
        pdb=" N   PRO D 211 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO D 211 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 211 "    0.036 5.00e-02 4.00e+02
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 4785
        2.90 -     3.40: 11507
        3.40 -     3.90: 20553
        3.90 -     4.40: 22860
        4.40 -     4.90: 40526
  Nonbonded interactions: 100231
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  38 "
            pdb=" OE2 GLU E  77 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" OE2 GLU B  77 "
            pdb=" OH  TYR C  38 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" ND2 ASN E  60 "
            pdb=" OD1 ASN E  89 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" ND2 ASN B  60 "
            pdb=" OD1 ASN B  89 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" ND2 ASN A  60 "
            pdb=" OD1 ASN A  89 "
     model   vdw
     2.401 3.120
  ... (remaining 100226 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.130
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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      :  0.019   0.903  12885  Z= 1.816
  Angle     :  0.838   7.289  17545  Z= 0.521
  Chirality :  0.057   0.206   1950
  Planarity :  0.008   0.069   2235
  Dihedral  : 14.033  89.566   4620
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  2.40 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.20), residues: 1525
  helix: -0.41 (0.20), residues: 500
  sheet: -0.17 (0.25), residues: 485
  loop : -2.72 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 123 
 TYR   0.009   0.001   TYR E 204 
 PHE   0.015   0.002   PHE D 304 
 TRP   0.026   0.001   TRP B 206 
 HIS   0.001   0.000   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (12880)
  covalent geometry    : angle       0.83842 (17545)
  hydrogen bonds       : bond        0.18626 (  551)
  hydrogen bonds       : angle       7.58264 ( 1731)
  Misc. bond           : bond        0.90231 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 179
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8377 (t0) cc_final: 0.8089 (t0)
REVERT: A   65 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6724 (ttt180)
REVERT: A  158 ASP cc_start: 0.5990 (m-30) cc_final: 0.5737 (m-30)
REVERT: B   27 ASN cc_start: 0.8458 (t0) cc_final: 0.8092 (t0)
REVERT: B   65 ARG cc_start: 0.7348 (ttm170) cc_final: 0.6904 (ttt180)
REVERT: B  158 ASP cc_start: 0.6004 (m-30) cc_final: 0.5794 (m-30)
REVERT: C   27 ASN cc_start: 0.8486 (t0) cc_final: 0.8166 (t0)
REVERT: C   65 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6856 (ttt180)
REVERT: C  158 ASP cc_start: 0.5938 (m-30) cc_final: 0.5732 (m-30)
REVERT: C  247 PHE cc_start: 0.7138 (m-80) cc_final: 0.6631 (t80)
REVERT: D   27 ASN cc_start: 0.8395 (t0) cc_final: 0.7994 (t0)
REVERT: D   65 ARG cc_start: 0.7302 (ttm170) cc_final: 0.6819 (ttt180)
REVERT: D  158 ASP cc_start: 0.5987 (m-30) cc_final: 0.5773 (m-30)
REVERT: E   27 ASN cc_start: 0.8451 (t0) cc_final: 0.8081 (t0)
REVERT: E   62 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: E   65 ARG cc_start: 0.7403 (ttm170) cc_final: 0.6926 (ttt180)
REVERT: E  158 ASP cc_start: 0.6181 (m-30) cc_final: 0.5924 (m-30)
  outliers start: 5
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1168
  time to fit residues: 30.2327
Evaluate side-chains
  136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0770
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.1980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
C 184 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.133173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.121948 restraints weight = 14968.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.123414 restraints weight = 11163.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.124487 restraints weight = 8783.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.124735 restraints weight = 7407.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.125036 restraints weight = 7024.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12885  Z= 0.125
  Angle     :  0.521   4.987  17545  Z= 0.277
  Chirality :  0.045   0.125   1950
  Planarity :  0.005   0.058   2235
  Dihedral  :  4.264  19.749   1690
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.02 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.21), residues: 1525
  helix:  1.17 (0.22), residues: 515
  sheet: -0.03 (0.25), residues: 465
  loop : -2.62 (0.22), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 255 
 TYR   0.010   0.001   TYR B  38 
 PHE   0.022   0.002   PHE C 282 
 TRP   0.018   0.001   TRP B 206 
 HIS   0.001   0.000   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (12880)
  covalent geometry    : angle       0.52101 (17545)
  hydrogen bonds       : bond        0.03945 (  551)
  hydrogen bonds       : angle       5.02618 ( 1731)
  Misc. bond           : bond        0.00023 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8445 (t0) cc_final: 0.8102 (t0)
REVERT: A   65 ARG cc_start: 0.7266 (ttm170) cc_final: 0.6791 (ttt180)
REVERT: A  158 ASP cc_start: 0.6082 (m-30) cc_final: 0.5773 (m-30)
REVERT: B   27 ASN cc_start: 0.8527 (t0) cc_final: 0.8116 (t0)
REVERT: B   62 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7587 (tm-30)
REVERT: B   65 ARG cc_start: 0.7384 (ttm170) cc_final: 0.6980 (ttt180)
REVERT: B  158 ASP cc_start: 0.6247 (m-30) cc_final: 0.5967 (m-30)
REVERT: C   27 ASN cc_start: 0.8548 (t0) cc_final: 0.8199 (t0)
REVERT: C   65 ARG cc_start: 0.7409 (ttm170) cc_final: 0.6967 (ttt180)
REVERT: C  158 ASP cc_start: 0.6287 (m-30) cc_final: 0.5968 (m-30)
REVERT: C  266 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8752 (mt)
REVERT: D   27 ASN cc_start: 0.8475 (t0) cc_final: 0.8081 (t0)
REVERT: D   65 ARG cc_start: 0.7354 (ttm170) cc_final: 0.6819 (ttt180)
REVERT: D   87 THR cc_start: 0.8663 (t) cc_final: 0.8102 (m)
REVERT: D  158 ASP cc_start: 0.6257 (m-30) cc_final: 0.6003 (m-30)
REVERT: E   27 ASN cc_start: 0.8520 (t0) cc_final: 0.8125 (t0)
REVERT: E   62 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7817 (tm-30)
REVERT: E   65 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6852 (ttt180)
REVERT: E  158 ASP cc_start: 0.6296 (m-30) cc_final: 0.6049 (m-30)
REVERT: E  239 MET cc_start: 0.6521 (ttp) cc_final: 0.6266 (ttp)
  outliers start: 11
  outliers final: 10
  residues processed: 160
  average time/residue: 0.1059
  time to fit residues: 24.5296
Evaluate side-chains
  145 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  266 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 126 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 139 GLN
E 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.123730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.112267 restraints weight = 15579.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.112290 restraints weight = 12351.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.112290 restraints weight = 12267.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.112290 restraints weight = 12267.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.112290 restraints weight = 12267.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12885  Z= 0.242
  Angle     :  0.616   7.556  17545  Z= 0.331
  Chirality :  0.049   0.151   1950
  Planarity :  0.005   0.062   2235
  Dihedral  :  4.652  18.394   1690
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.16 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.21), residues: 1525
  helix:  1.42 (0.22), residues: 485
  sheet: -0.33 (0.24), residues: 495
  loop : -2.23 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 255 
 TYR   0.013   0.002   TYR D 204 
 PHE   0.019   0.002   PHE C 247 
 TRP   0.016   0.002   TRP D 206 
 HIS   0.001   0.000   HIS E 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 (12880)
  covalent geometry    : angle       0.61648 (17545)
  hydrogen bonds       : bond        0.05087 (  551)
  hydrogen bonds       : angle       5.15055 ( 1731)
  Misc. bond           : bond        0.00041 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8496 (t0) cc_final: 0.8125 (t0)
REVERT: A   65 ARG cc_start: 0.7310 (ttm170) cc_final: 0.6824 (ttt180)
REVERT: B   27 ASN cc_start: 0.8536 (t0) cc_final: 0.8310 (t0)
REVERT: B   62 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: B   65 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7093 (ttt180)
REVERT: C   65 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6990 (ttt180)
REVERT: D   27 ASN cc_start: 0.8497 (t0) cc_final: 0.8177 (t0)
REVERT: D   65 ARG cc_start: 0.7500 (ttm170) cc_final: 0.6949 (ttt180)
REVERT: E   27 ASN cc_start: 0.8579 (t0) cc_final: 0.8188 (t0)
REVERT: E   62 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: E   65 ARG cc_start: 0.7518 (ttm170) cc_final: 0.6982 (ttt180)
  outliers start: 21
  outliers final: 21
  residues processed: 186
  average time/residue: 0.1012
  time to fit residues: 27.6318
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  161 TRP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  266 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 133 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.126636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.115703 restraints weight = 15295.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115741 restraints weight = 11928.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115741 restraints weight = 11620.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115741 restraints weight = 11620.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115741 restraints weight = 11620.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12885  Z= 0.135
  Angle     :  0.512   5.802  17545  Z= 0.271
  Chirality :  0.046   0.140   1950
  Planarity :  0.004   0.057   2235
  Dihedral  :  4.251  16.675   1690
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 12.15 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.22), residues: 1525
  helix:  1.92 (0.22), residues: 485
  sheet: -0.20 (0.24), residues: 495
  loop : -2.19 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 123 
 TYR   0.009   0.001   TYR C 245 
 PHE   0.019   0.002   PHE D 282 
 TRP   0.017   0.001   TRP B 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12880)
  covalent geometry    : angle       0.51153 (17545)
  hydrogen bonds       : bond        0.03824 (  551)
  hydrogen bonds       : angle       4.78192 ( 1731)
  Misc. bond           : bond        0.00012 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8475 (t0) cc_final: 0.8076 (t0)
REVERT: A   65 ARG cc_start: 0.7267 (ttm170) cc_final: 0.6759 (ttt180)
REVERT: B   27 ASN cc_start: 0.8498 (t0) cc_final: 0.8150 (t0)
REVERT: B   62 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: B   65 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7016 (ttt180)
REVERT: C   65 ARG cc_start: 0.7440 (ttm170) cc_final: 0.6907 (ttt180)
REVERT: D   27 ASN cc_start: 0.8449 (t0) cc_final: 0.8094 (t0)
REVERT: D   65 ARG cc_start: 0.7377 (ttm170) cc_final: 0.6864 (ttt180)
REVERT: E   27 ASN cc_start: 0.8515 (t0) cc_final: 0.8133 (t0)
REVERT: E   62 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: E   65 ARG cc_start: 0.7498 (ttm170) cc_final: 0.6949 (ttt180)
  outliers start: 14
  outliers final: 12
  residues processed: 171
  average time/residue: 0.0925
  time to fit residues: 23.8729
Evaluate side-chains
  163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  266 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 138 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 87 optimal weight:    0.3980
   chunk 133 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 99 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 146 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.0386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.128073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.117130 restraints weight = 15292.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.117168 restraints weight = 11671.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.117168 restraints weight = 11524.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.117168 restraints weight = 11524.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.117168 restraints weight = 11524.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12885  Z= 0.116
  Angle     :  0.492   5.182  17545  Z= 0.260
  Chirality :  0.045   0.135   1950
  Planarity :  0.004   0.054   2235
  Dihedral  :  4.044  16.508   1690
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.53 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.22), residues: 1525
  helix:  2.12 (0.22), residues: 485
  sheet:  0.00 (0.24), residues: 495
  loop : -2.16 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 123 
 TYR   0.009   0.001   TYR C 245 
 PHE   0.013   0.001   PHE C 247 
 TRP   0.018   0.001   TRP C 206 
 HIS   0.001   0.000   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (12880)
  covalent geometry    : angle       0.49153 (17545)
  hydrogen bonds       : bond        0.03524 (  551)
  hydrogen bonds       : angle       4.58567 ( 1731)
  Misc. bond           : bond        0.00014 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8426 (t0) cc_final: 0.8061 (t0)
REVERT: A   65 ARG cc_start: 0.7196 (ttm170) cc_final: 0.6740 (ttt180)
REVERT: A  266 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8864 (mt)
REVERT: B   27 ASN cc_start: 0.8478 (t0) cc_final: 0.8137 (t0)
REVERT: B   65 ARG cc_start: 0.7501 (ttm170) cc_final: 0.6930 (ttt180)
REVERT: B  266 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8858 (mt)
REVERT: C   62 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7320 (tm-30)
REVERT: D   27 ASN cc_start: 0.8421 (t0) cc_final: 0.8098 (t0)
REVERT: D   65 ARG cc_start: 0.7293 (ttm170) cc_final: 0.6816 (ttt180)
REVERT: E   27 ASN cc_start: 0.8468 (t0) cc_final: 0.8112 (t0)
REVERT: E   65 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6815 (ttt180)
  outliers start: 20
  outliers final: 15
  residues processed: 176
  average time/residue: 0.0936
  time to fit residues: 24.5546
Evaluate side-chains
  169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  158 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  266 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 119 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 136 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 146 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 57 optimal weight:    0.4980
   chunk 85 optimal weight:    0.8980
   chunk 148 optimal weight:   10.0000
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.126001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.114795 restraints weight = 15365.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.115225 restraints weight = 13461.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.115225 restraints weight = 11767.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.115225 restraints weight = 11767.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.115225 restraints weight = 11767.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12885  Z= 0.150
  Angle     :  0.523   5.859  17545  Z= 0.279
  Chirality :  0.046   0.135   1950
  Planarity :  0.004   0.054   2235
  Dihedral  :  4.139  16.718   1690
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.96 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.22), residues: 1525
  helix:  2.06 (0.22), residues: 485
  sheet: -0.06 (0.24), residues: 495
  loop : -2.15 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 123 
 TYR   0.012   0.001   TYR B  38 
 PHE   0.019   0.001   PHE E 282 
 TRP   0.017   0.001   TRP A 206 
 HIS   0.001   0.000   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (12880)
  covalent geometry    : angle       0.52305 (17545)
  hydrogen bonds       : bond        0.03851 (  551)
  hydrogen bonds       : angle       4.62575 ( 1731)
  Misc. bond           : bond        0.00018 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8388 (t0) cc_final: 0.8048 (t0)
REVERT: A   65 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6753 (ttt180)
REVERT: A  266 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8898 (mt)
REVERT: B   27 ASN cc_start: 0.8457 (t0) cc_final: 0.8122 (t0)
REVERT: B   62 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7648 (tm-30)
REVERT: B   65 ARG cc_start: 0.7518 (ttm170) cc_final: 0.7110 (ttt180)
REVERT: B  266 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8896 (mt)
REVERT: C   62 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7348 (tm-30)
REVERT: C   65 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7337 (ttt180)
REVERT: C  266 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8851 (mt)
REVERT: D   27 ASN cc_start: 0.8388 (t0) cc_final: 0.8074 (t0)
REVERT: D   65 ARG cc_start: 0.7374 (ttm170) cc_final: 0.6890 (ttt180)
REVERT: E   27 ASN cc_start: 0.8479 (t0) cc_final: 0.8131 (t0)
REVERT: E   62 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7681 (tm-30)
REVERT: E   65 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6979 (ttt180)
  outliers start: 29
  outliers final: 22
  residues processed: 181
  average time/residue: 0.0902
  time to fit residues: 24.4224
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  158 ASP
Chi-restraints excluded: chain A residue  161 TRP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  266 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0370
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 132 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0070
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.129004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.118365 restraints weight = 15140.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.118975 restraints weight = 11673.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.119033 restraints weight = 10170.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.120361 restraints weight = 10064.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.120418 restraints weight = 8325.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12885  Z= 0.105
  Angle     :  0.481   4.722  17545  Z= 0.256
  Chirality :  0.045   0.126   1950
  Planarity :  0.004   0.052   2235
  Dihedral  :  3.884  15.727   1690
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.91 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.22), residues: 1525
  helix:  2.20 (0.22), residues: 490
  sheet:  0.14 (0.24), residues: 495
  loop : -2.11 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 123 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.018   0.001   PHE B 282 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (12880)
  covalent geometry    : angle       0.48123 (17545)
  hydrogen bonds       : bond        0.03223 (  551)
  hydrogen bonds       : angle       4.39956 ( 1731)
  Misc. bond           : bond        0.00013 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8379 (t0) cc_final: 0.8012 (t0)
REVERT: A   65 ARG cc_start: 0.7162 (ttm170) cc_final: 0.6754 (ttt180)
REVERT: B   27 ASN cc_start: 0.8435 (t0) cc_final: 0.8210 (t0)
REVERT: B   62 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7589 (tm-30)
REVERT: B   65 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7056 (ttt180)
REVERT: C   62 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7148 (tm-30)
REVERT: C   65 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7261 (ttt180)
REVERT: D   27 ASN cc_start: 0.8369 (t0) cc_final: 0.8033 (t0)
REVERT: D   62 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: D   65 ARG cc_start: 0.7278 (ttm170) cc_final: 0.6773 (ttt180)
REVERT: E   27 ASN cc_start: 0.8445 (t0) cc_final: 0.8110 (t0)
REVERT: E   62 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: E   65 ARG cc_start: 0.7381 (ttm170) cc_final: 0.6930 (ttt180)
REVERT: E  239 MET cc_start: 0.7213 (ttp) cc_final: 0.6933 (tmm)
  outliers start: 31
  outliers final: 19
  residues processed: 180
  average time/residue: 0.0948
  time to fit residues: 25.5260
Evaluate side-chains
  161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 144 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 67 optimal weight:    0.3980
   chunk 16 optimal weight:    6.9990
   chunk 117 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0470
   overall best weight:    0.9680

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.128417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.118096 restraints weight = 15171.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.118096 restraints weight = 11622.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.118096 restraints weight = 11622.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.118096 restraints weight = 11622.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.118096 restraints weight = 11622.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12885  Z= 0.115
  Angle     :  0.502   6.753  17545  Z= 0.268
  Chirality :  0.045   0.127   1950
  Planarity :  0.004   0.051   2235
  Dihedral  :  3.858  15.384   1690
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.42 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.22), residues: 1525
  helix:  2.21 (0.22), residues: 490
  sheet:  0.29 (0.25), residues: 465
  loop : -2.02 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 123 
 TYR   0.010   0.001   TYR B  38 
 PHE   0.016   0.001   PHE C 247 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12880)
  covalent geometry    : angle       0.50245 (17545)
  hydrogen bonds       : bond        0.03285 (  551)
  hydrogen bonds       : angle       4.35611 ( 1731)
  Misc. bond           : bond        0.00014 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8286 (t0) cc_final: 0.7984 (t0)
REVERT: A   65 ARG cc_start: 0.7246 (ttm170) cc_final: 0.6786 (ttt180)
REVERT: B   62 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: B   65 ARG cc_start: 0.7506 (ttm170) cc_final: 0.7087 (ttt180)
REVERT: B  245 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8010 (m-80)
REVERT: C   62 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7098 (tm-30)
REVERT: C   65 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7289 (ttt180)
REVERT: D   27 ASN cc_start: 0.8324 (t0) cc_final: 0.8013 (t0)
REVERT: D   62 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7259 (tm-30)
REVERT: D   65 ARG cc_start: 0.7281 (ttm170) cc_final: 0.6777 (ttt180)
REVERT: E   27 ASN cc_start: 0.8423 (t0) cc_final: 0.8070 (t0)
REVERT: E   62 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: E   65 ARG cc_start: 0.7375 (ttm170) cc_final: 0.6918 (ttt180)
REVERT: E  239 MET cc_start: 0.7217 (ttp) cc_final: 0.6928 (tmm)
  outliers start: 28
  outliers final: 21
  residues processed: 171
  average time/residue: 0.0946
  time to fit residues: 24.2093
Evaluate side-chains
  166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 108 optimal weight:    5.9990
   chunk 138 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 116 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0570
   chunk 87 optimal weight:    7.9990
   overall best weight:    0.6500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.130019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.119554 restraints weight = 15132.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.119999 restraints weight = 11499.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.121726 restraints weight = 10303.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.122315 restraints weight = 8432.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.122392 restraints weight = 7311.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12885  Z= 0.102
  Angle     :  0.486   5.658  17545  Z= 0.258
  Chirality :  0.045   0.123   1950
  Planarity :  0.004   0.050   2235
  Dihedral  :  3.726  15.153   1690
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.93 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.22), residues: 1525
  helix:  2.27 (0.22), residues: 490
  sheet:  0.41 (0.25), residues: 465
  loop : -2.00 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 123 
 TYR   0.010   0.001   TYR B  38 
 PHE   0.015   0.001   PHE C 247 
 TRP   0.019   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (12880)
  covalent geometry    : angle       0.48551 (17545)
  hydrogen bonds       : bond        0.03031 (  551)
  hydrogen bonds       : angle       4.23399 ( 1731)
  Misc. bond           : bond        0.00011 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8304 (t0) cc_final: 0.7966 (t0)
REVERT: A   65 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6813 (ttt180)
REVERT: A  266 ILE cc_start: 0.9014 (mm) cc_final: 0.8807 (mt)
REVERT: B   62 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: B   65 ARG cc_start: 0.7474 (ttm170) cc_final: 0.7047 (ttt180)
REVERT: B  245 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7862 (m-80)
REVERT: C   62 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7112 (tm-30)
REVERT: C   65 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7177 (ttt180)
REVERT: D   27 ASN cc_start: 0.8326 (t0) cc_final: 0.8050 (t0)
REVERT: D   62 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7262 (tm-30)
REVERT: D   65 ARG cc_start: 0.7293 (ttm170) cc_final: 0.6765 (ttt180)
REVERT: E   27 ASN cc_start: 0.8390 (t0) cc_final: 0.8095 (t0)
REVERT: E   65 ARG cc_start: 0.7324 (ttm170) cc_final: 0.6803 (ttt180)
REVERT: E  245 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7911 (m-80)
  outliers start: 26
  outliers final: 23
  residues processed: 170
  average time/residue: 0.1024
  time to fit residues: 25.7700
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  239 MET
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 140 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.128371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.117551 restraints weight = 15273.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.118707 restraints weight = 13164.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.119814 restraints weight = 10429.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.120343 restraints weight = 8677.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.120488 restraints weight = 7676.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12885  Z= 0.121
  Angle     :  0.502   5.372  17545  Z= 0.267
  Chirality :  0.045   0.132   1950
  Planarity :  0.004   0.050   2235
  Dihedral  :  3.794  14.982   1690
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.21 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.07 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.22), residues: 1525
  helix:  2.23 (0.22), residues: 490
  sheet:  0.37 (0.25), residues: 465
  loop : -1.97 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 123 
 TYR   0.010   0.001   TYR B  38 
 PHE   0.018   0.001   PHE C 247 
 TRP   0.019   0.001   TRP A 206 
 HIS   0.001   0.000   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12880)
  covalent geometry    : angle       0.50157 (17545)
  hydrogen bonds       : bond        0.03293 (  551)
  hydrogen bonds       : angle       4.28463 ( 1731)
  Misc. bond           : bond        0.00015 (    5)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8293 (t0) cc_final: 0.7968 (t0)
REVERT: A   65 ARG cc_start: 0.7256 (ttm170) cc_final: 0.6836 (ttt180)
REVERT: B   62 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: B   65 ARG cc_start: 0.7444 (ttm170) cc_final: 0.7034 (ttt180)
REVERT: B  245 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8010 (m-80)
REVERT: C   65 ARG cc_start: 0.7665 (ttm170) cc_final: 0.7266 (ttt180)
REVERT: D   27 ASN cc_start: 0.8321 (t0) cc_final: 0.8036 (t0)
REVERT: D   62 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7522 (tm-30)
REVERT: D   65 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6889 (ttt180)
REVERT: D  245 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7834 (m-80)
REVERT: E   27 ASN cc_start: 0.8382 (t0) cc_final: 0.8093 (t0)
REVERT: E   65 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6874 (ttt180)
REVERT: E  239 MET cc_start: 0.7246 (ttp) cc_final: 0.7022 (tmm)
REVERT: E  245 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7944 (m-80)
  outliers start: 28
  outliers final: 23
  residues processed: 165
  average time/residue: 0.1056
  time to fit residues: 25.6794
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  219 SER
Chi-restraints excluded: chain E residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 113 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.124293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.113833 restraints weight = 15421.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.114458 restraints weight = 11881.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.114459 restraints weight = 10321.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.114459 restraints weight = 10320.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.114470 restraints weight = 10320.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12885  Z= 0.171
  Angle     :  0.553   5.482  17545  Z= 0.295
  Chirality :  0.047   0.141   1950
  Planarity :  0.004   0.051   2235
  Dihedral  :  4.164  15.780   1690
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.87 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.85 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.21), residues: 1525
  helix:  2.08 (0.22), residues: 485
  sheet:  0.16 (0.25), residues: 465
  loop : -2.03 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 123 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.023   0.002   PHE C 247 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12880)
  covalent geometry    : angle       0.55283 (17545)
  hydrogen bonds       : bond        0.04053 (  551)
  hydrogen bonds       : angle       4.56704 ( 1731)
  Misc. bond           : bond        0.00027 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1498.75 seconds
wall clock time: 26 minutes 47.61 seconds (1607.61 seconds total)