Starting phenix.real_space_refine
on Wed Feb  4 19:24:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngq_49390/02_2026/9ngq_49390_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngq_49390/02_2026/9ngq_49390.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/9ngq_49390/02_2026/9ngq_49390_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngq_49390/02_2026/9ngq_49390_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngq_49390/02_2026/9ngq_49390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngq_49390/02_2026/9ngq_49390.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-2.0-5952/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: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 8
          Unusual residues: {' NA': 4, '3CN': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' NA': 1, '3CN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
    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: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' NA': 1, '3CN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.17, per 1000 atoms: 0.25
  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 578.6 milliseconds
  

  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:
      45 helices and 15 sheets defined
      34.5% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  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 249
      removed outlier: 3.600A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR A 241 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR A 249 " --> pdb=" O   TYR A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 252
      No H-bonds generated for 'chain 'A' and resid 250 through 252'
    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 249
      removed outlier: 3.600A  pdb=" N   ARG B 231 " --> pdb=" O   SER B 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE B 247 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TYR B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR B 249 " --> pdb=" O   TYR B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 252
      No H-bonds generated for 'chain 'B' and resid 250 through 252'
    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 249
      removed outlier: 3.600A  pdb=" N   ARG C 231 " --> pdb=" O   SER C 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR C 241 " --> pdb=" O   THR C 237 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR C 248 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR C 249 " --> pdb=" O   TYR C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 252
      No H-bonds generated for 'chain 'C' and resid 250 through 252'
    Processing helix  chain 'C' and resid 260 through 285
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 3.596A  pdb=" N   ILE C 317 " --> pdb=" O   CYS C 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 4.140A  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 249
      removed outlier: 3.600A  pdb=" N   ARG D 231 " --> pdb=" O   SER D 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR D 241 " --> pdb=" O   THR D 237 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE D 247 " --> pdb=" O   VAL D 243 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TYR D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR D 249 " --> pdb=" O   TYR D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 252
      No H-bonds generated for 'chain 'D' and resid 250 through 252'
    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: 4.139A  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 249
      removed outlier: 3.599A  pdb=" N   ARG E 231 " --> pdb=" O   SER E 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR E 241 " --> pdb=" O   THR E 237 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE E 247 " --> pdb=" O   VAL E 243 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR E 248 " --> pdb=" O   ALA E 244 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR E 249 " --> pdb=" O   TYR E 245 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 252
      No H-bonds generated for 'chain 'E' and resid 250 through 252'
    Processing helix  chain 'E' and resid 260 through 285
    Processing helix  chain 'E' and resid 303 through 317
      removed outlier: 3.596A  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: 6.851A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 82
      removed outlier: 4.124A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 7.591A  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: 6.475A  pdb=" N   PHE B 188 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   SER B 171 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ARG B 190 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   HIS B 169 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   THR B 192 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   SER B 167 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 6.774A  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: 4.216A  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: 6.868A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.850A  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: 3.717A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 3.511A  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: 3.511A  pdb=" N   GLY C  37 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 3.717A  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: 7.592A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.194A  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: 6.475A  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: 6.278A  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: 6.773A  pdb=" N   ARG C 194 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   LYS C 165 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.217A  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: 4.552A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.850A  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: 6.344A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
      removed outlier: 4.125A  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: 3.512A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D 106 " (cutoff:3.500A)
      removed outlier: 3.717A  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: 7.592A  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: 6.476A  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: 6.603A  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: 6.272A  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: 6.867A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.344A  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: 3.512A  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: 3.512A  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: 4.354A  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: 6.476A  pdb=" N   PHE E 188 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   SER E 171 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG E 190 " --> pdb=" O   HIS E 169 " (cutoff:3.500A)
      removed outlier: 6.604A  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: 6.274A  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: 6.590A  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)

    577 hydrogen bonds defined for protein.
    1662 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: 2.18

  Time building geometry restraints manager: 1.38 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: 3982
        1.34 -     1.46: 2649
        1.46 -     1.57: 6199
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" N   ILE E 162 "
       pdb=" CA  ILE E 162 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.17e-02 7.31e+03 9.29e+00
  bond pdb=" N   ILE D 162 "
       pdb=" CA  ILE D 162 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.17e-02 7.31e+03 9.12e+00
  bond pdb=" N   ILE C 162 "
       pdb=" CA  ILE C 162 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.17e-02 7.31e+03 8.96e+00
  bond pdb=" N   ILE A 162 "
       pdb=" CA  ILE A 162 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.17e-02 7.31e+03 8.94e+00
  bond pdb=" N   ILE B 162 "
       pdb=" CA  ILE B 162 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.17e-02 7.31e+03 8.69e+00
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 16484
        1.46 -     2.91: 846
        2.91 -     4.37: 150
        4.37 -     5.83: 45
        5.83 -     7.28: 20
  Bond angle restraints: 17545
  Sorted by residual:
  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
  angle pdb=" CA  ASP E 158 "
        pdb=" CB  ASP E 158 "
        pdb=" CG  ASP E 158 "
      ideal   model   delta    sigma   weight residual
     112.60  116.15   -3.55 1.00e+00 1.00e+00 1.26e+01
  angle pdb=" CA  ASP D 158 "
        pdb=" CB  ASP D 158 "
        pdb=" CG  ASP D 158 "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -3.54 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" CA  ASP B 158 "
        pdb=" CB  ASP B 158 "
        pdb=" CG  ASP B 158 "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -3.54 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" CA  ASP C 158 "
        pdb=" CB  ASP C 158 "
        pdb=" CG  ASP C 158 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 6790
       17.92 -    35.85: 622
       35.85 -    53.77: 83
       53.77 -    71.70: 30
       71.70 -    89.62: 5
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  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 -156.00  -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 E 227 "
           pdb=" C   SER E 227 "
           pdb=" N   PHE E 228 "
           pdb=" CA  PHE E 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 -    0.040: 1207
       0.040 -    0.080: 441
       0.080 -    0.121: 228
       0.121 -    0.161: 54
       0.161 -    0.201: 20
  Chirality restraints: 1950
  Sorted by residual:
  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
  chirality pdb=" CA  ILE B 157 "
            pdb=" N   ILE B 157 "
            pdb=" C   ILE B 157 "
            pdb=" CB  ILE B 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
  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    2.63   -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 6.44e+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 C 210 "   -0.042 5.00e-02 4.00e+02   6.34e-02 6.42e+00
        pdb=" N   PRO C 211 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO C 211 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 211 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 210 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.42e+00
        pdb=" N   PRO A 211 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 211 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 211 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 931
        2.74 -     3.28: 11703
        3.28 -     3.82: 20553
        3.82 -     4.36: 24004
        4.36 -     4.90: 42881
  Nonbonded interactions: 100072
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 131 "
            pdb=" ND  3CN D 401 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OE2 GLU C 131 "
            pdb=" ND  3CN C 401 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OE2 GLU B 131 "
            pdb=" ND  3CN B 401 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OE2 GLU E 131 "
            pdb=" ND  3CN E 401 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" ND2 ASN B  60 "
            pdb=" OD1 ASN B  89 "
     model   vdw
     2.401 3.120
  ... (remaining 100067 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 11 through 401)
  selection = (chain 'B' and resid 11 through 401)
  selection = chain 'C'
  selection = chain 'D'
  selection = (chain 'E' and resid 11 through 401)
}

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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.400
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
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      :  0.010   0.902  12881  Z= 0.846
  Angle     :  0.778   7.282  17545  Z= 0.445
  Chirality :  0.055   0.201   1950
  Planarity :  0.008   0.069   2235
  Dihedral  : 14.013  89.622   4620
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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 are not related in a simple way.
  whole: -1.59 (0.20), residues: 1525
  helix: -0.40 (0.21), residues: 505
  sheet: -0.17 (0.25), residues: 485
  loop : -2.46 (0.22), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 123 
 TYR   0.009   0.001   TYR A 204 
 PHE   0.015   0.002   PHE B 304 
 TRP   0.025   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (12880)
  covalent geometry    : angle       0.77825 (17545)
  hydrogen bonds       : bond        0.16921 (  527)
  hydrogen bonds       : angle       7.35204 ( 1662)
  Misc. bond           : bond        0.90192 (    1)

*********************** 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
  189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8329 (t0) cc_final: 0.8022 (t0)
REVERT: A   65 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6720 (ttt180)
REVERT: A  158 ASP cc_start: 0.6034 (m-30) cc_final: 0.5780 (m-30)
REVERT: B   27 ASN cc_start: 0.8408 (t0) cc_final: 0.8022 (t0)
REVERT: B   65 ARG cc_start: 0.7331 (ttm170) cc_final: 0.6878 (ttt180)
REVERT: B  158 ASP cc_start: 0.6053 (m-30) cc_final: 0.5836 (m-30)
REVERT: C   27 ASN cc_start: 0.8450 (t0) cc_final: 0.8102 (t0)
REVERT: C   65 ARG cc_start: 0.7342 (ttm170) cc_final: 0.6884 (ttt180)
REVERT: C  158 ASP cc_start: 0.6064 (m-30) cc_final: 0.5799 (m-30)
REVERT: D   27 ASN cc_start: 0.8385 (t0) cc_final: 0.7947 (t0)
REVERT: D   65 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6838 (ttt180)
REVERT: D  158 ASP cc_start: 0.6034 (m-30) cc_final: 0.5807 (m-30)
REVERT: E   27 ASN cc_start: 0.8410 (t0) cc_final: 0.8020 (t0)
REVERT: E   65 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6895 (ttt180)
REVERT: E  158 ASP cc_start: 0.6206 (m-30) cc_final: 0.5936 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1231
  time to fit residues: 33.1734
Evaluate side-chains
  140 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.0980
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0070
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.5398

-------------------------------------------------------------------------------
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 = 0.3294 r_free = 0.3294 target = 0.133158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.122077 restraints weight = 15042.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.122097 restraints weight = 12134.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.122097 restraints weight = 11988.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.122097 restraints weight = 11988.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.122097 restraints weight = 11988.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12881  Z= 0.104
  Angle     :  0.503   4.475  17545  Z= 0.267
  Chirality :  0.045   0.127   1950
  Planarity :  0.004   0.056   2235
  Dihedral  :  4.299  21.427   1690
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  5.82 %
    Favored  : 93.75 %
  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 are not related in a simple way.
  whole: -0.82 (0.21), residues: 1525
  helix:  0.85 (0.23), residues: 500
  sheet:  0.03 (0.26), residues: 465
  loop : -2.36 (0.22), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 255 
 TYR   0.012   0.001   TYR D 245 
 PHE   0.016   0.001   PHE B 282 
 TRP   0.019   0.001   TRP C 206 
 HIS   0.001   0.000   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (12880)
  covalent geometry    : angle       0.50344 (17545)
  hydrogen bonds       : bond        0.03569 (  527)
  hydrogen bonds       : angle       5.00758 ( 1662)
  Misc. bond           : bond        0.00029 (    1)

*********************** 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
  188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 182
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8339 (t0) cc_final: 0.7997 (t0)
REVERT: A   65 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6770 (ttt180)
REVERT: A  158 ASP cc_start: 0.6033 (m-30) cc_final: 0.5726 (m-30)
REVERT: B   27 ASN cc_start: 0.8421 (t0) cc_final: 0.8052 (t0)
REVERT: B   62 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: B   65 ARG cc_start: 0.7418 (ttm170) cc_final: 0.7005 (ttt180)
REVERT: B  158 ASP cc_start: 0.6165 (m-30) cc_final: 0.5865 (m-30)
REVERT: C   27 ASN cc_start: 0.8455 (t0) cc_final: 0.8117 (t0)
REVERT: C   65 ARG cc_start: 0.7441 (ttm170) cc_final: 0.6942 (ttt180)
REVERT: C  158 ASP cc_start: 0.6231 (m-30) cc_final: 0.5916 (m-30)
REVERT: D   27 ASN cc_start: 0.8404 (t0) cc_final: 0.7973 (t0)
REVERT: D   65 ARG cc_start: 0.7392 (ttm170) cc_final: 0.6840 (ttt180)
REVERT: D   87 THR cc_start: 0.8689 (t) cc_final: 0.8024 (m)
REVERT: D  158 ASP cc_start: 0.6199 (m-30) cc_final: 0.5943 (m-30)
REVERT: E   27 ASN cc_start: 0.8453 (t0) cc_final: 0.8035 (t0)
REVERT: E   65 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6844 (ttt180)
REVERT: E  158 ASP cc_start: 0.6286 (m-30) cc_final: 0.6043 (m-30)
  outliers start: 6
  outliers final: 6
  residues processed: 188
  average time/residue: 0.1140
  time to fit residues: 31.3429
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 164
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue  266 ILE
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:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 88 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 126 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.3185 r_free = 0.3185 target = 0.124172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.112584 restraints weight = 15661.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.112734 restraints weight = 12998.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.113249 restraints weight = 12382.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.113224 restraints weight = 11769.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.113224 restraints weight = 11409.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12881  Z= 0.210
  Angle     :  0.580   4.580  17545  Z= 0.312
  Chirality :  0.048   0.148   1950
  Planarity :  0.005   0.060   2235
  Dihedral  :  4.943  50.426   1690
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.75 %
    Favored  : 88.58 %
  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 are not related in a simple way.
  whole: -0.52 (0.22), residues: 1525
  helix:  1.33 (0.24), residues: 475
  sheet: -0.22 (0.24), residues: 495
  loop : -1.93 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 123 
 TYR   0.012   0.002   TYR D 204 
 PHE   0.014   0.002   PHE C 304 
 TRP   0.015   0.001   TRP E 206 
 HIS   0.001   0.000   HIS D 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 (12880)
  covalent geometry    : angle       0.58004 (17545)
  hydrogen bonds       : bond        0.04134 (  527)
  hydrogen bonds       : angle       4.90434 ( 1662)
  Misc. bond           : bond        0.00057 (    1)

*********************** 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
  184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8446 (t0) cc_final: 0.8019 (t0)
REVERT: A   65 ARG cc_start: 0.7290 (ttm170) cc_final: 0.6833 (ttt180)
REVERT: A  161 TRP cc_start: 0.7413 (t60) cc_final: 0.7198 (t60)
REVERT: B   27 ASN cc_start: 0.8508 (t0) cc_final: 0.8252 (t0)
REVERT: B   62 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: B   65 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7059 (ttt180)
REVERT: B  158 ASP cc_start: 0.6357 (m-30) cc_final: 0.6155 (m-30)
REVERT: B  245 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8280 (m-80)
REVERT: C   27 ASN cc_start: 0.8504 (t0) cc_final: 0.8142 (t0)
REVERT: C   65 ARG cc_start: 0.7453 (ttm170) cc_final: 0.7008 (ttt180)
REVERT: C  158 ASP cc_start: 0.6407 (m-30) cc_final: 0.6182 (m-30)
REVERT: D   27 ASN cc_start: 0.8429 (t0) cc_final: 0.8018 (t0)
REVERT: D   65 ARG cc_start: 0.7470 (ttm170) cc_final: 0.6898 (ttt180)
REVERT: D   87 THR cc_start: 0.8763 (t) cc_final: 0.8256 (m)
REVERT: E   27 ASN cc_start: 0.8492 (t0) cc_final: 0.8070 (t0)
REVERT: E   65 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6954 (ttt180)
REVERT: E  158 ASP cc_start: 0.6581 (m-30) cc_final: 0.6341 (m-30)
  outliers start: 23
  outliers final: 21
  residues processed: 180
  average time/residue: 0.1043
  time to fit residues: 27.8572
Evaluate side-chains
  182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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 A residue  266 ILE
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 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  245 TYR
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   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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 133 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3212 r_free = 0.3212 target = 0.126352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.115373 restraints weight = 15353.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115669 restraints weight = 11940.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115669 restraints weight = 11033.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115669 restraints weight = 11033.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.115669 restraints weight = 11033.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12881  Z= 0.126
  Angle     :  0.503   4.722  17545  Z= 0.265
  Chirality :  0.046   0.138   1950
  Planarity :  0.004   0.056   2235
  Dihedral  :  4.706  54.416   1690
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.44 %
    Favored  : 85.89 %
  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 are not related in a simple way.
  whole: -0.22 (0.22), residues: 1525
  helix:  1.74 (0.24), residues: 475
  sheet: -0.11 (0.25), residues: 495
  loop : -1.86 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 123 
 TYR   0.008   0.001   TYR B  38 
 PHE   0.025   0.001   PHE C 282 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS C 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12880)
  covalent geometry    : angle       0.50329 (17545)
  hydrogen bonds       : bond        0.03436 (  527)
  hydrogen bonds       : angle       4.58108 ( 1662)
  Misc. bond           : bond        0.00015 (    1)

*********************** 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
  189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8446 (t0) cc_final: 0.8039 (t0)
REVERT: A   65 ARG cc_start: 0.7244 (ttm170) cc_final: 0.6764 (ttt180)
REVERT: A  158 ASP cc_start: 0.6158 (m-30) cc_final: 0.5952 (m-30)
REVERT: A  266 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8883 (mt)
REVERT: B   27 ASN cc_start: 0.8483 (t0) cc_final: 0.8106 (t0)
REVERT: B   62 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: B   65 ARG cc_start: 0.7497 (ttm170) cc_final: 0.6988 (ttt180)
REVERT: B  158 ASP cc_start: 0.6331 (m-30) cc_final: 0.6115 (m-30)
REVERT: B  245 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8005 (m-80)
REVERT: C   27 ASN cc_start: 0.8465 (t0) cc_final: 0.8134 (t0)
REVERT: C   65 ARG cc_start: 0.7435 (ttm170) cc_final: 0.6906 (ttt180)
REVERT: C  266 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8784 (mt)
REVERT: D   27 ASN cc_start: 0.8403 (t0) cc_final: 0.8003 (t0)
REVERT: D   65 ARG cc_start: 0.7408 (ttm170) cc_final: 0.6839 (ttt180)
REVERT: D  158 ASP cc_start: 0.6232 (m-30) cc_final: 0.6024 (m-30)
REVERT: E   27 ASN cc_start: 0.8498 (t0) cc_final: 0.8108 (t0)
REVERT: E   65 ARG cc_start: 0.7383 (ttm170) cc_final: 0.6920 (ttt180)
REVERT: E  158 ASP cc_start: 0.6497 (m-30) cc_final: 0.6264 (m-30)
  outliers start: 23
  outliers final: 20
  residues processed: 182
  average time/residue: 0.1114
  time to fit residues: 29.9421
Evaluate side-chains
  173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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 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  245 TYR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  245 TYR
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 138 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 99 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 146 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.3185 r_free = 0.3185 target = 0.123680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.114019 restraints weight = 15536.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.114763 restraints weight = 12382.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.115182 restraints weight = 10666.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.115213 restraints weight = 9795.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.115213 restraints weight = 9685.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12881  Z= 0.168
  Angle     :  0.538   4.699  17545  Z= 0.286
  Chirality :  0.047   0.142   1950
  Planarity :  0.004   0.057   2235
  Dihedral  :  4.831  59.897   1690
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.73 %
    Favored  : 84.87 %
  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 are not related in a simple way.
  whole: -0.29 (0.22), residues: 1525
  helix:  1.68 (0.24), residues: 475
  sheet: -0.20 (0.24), residues: 495
  loop : -1.84 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 123 
 TYR   0.010   0.001   TYR D 204 
 PHE   0.014   0.002   PHE C 282 
 TRP   0.017   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (12880)
  covalent geometry    : angle       0.53831 (17545)
  hydrogen bonds       : bond        0.03715 (  527)
  hydrogen bonds       : angle       4.60532 ( 1662)
  Misc. bond           : bond        0.00016 (    1)

*********************** 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
  199 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8409 (t0) cc_final: 0.8039 (t0)
REVERT: A   65 ARG cc_start: 0.7237 (ttm170) cc_final: 0.6773 (ttt180)
REVERT: A  266 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8893 (mt)
REVERT: B   27 ASN cc_start: 0.8439 (t0) cc_final: 0.8041 (t0)
REVERT: B   62 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: B   65 ARG cc_start: 0.7528 (ttm170) cc_final: 0.7073 (ttt180)
REVERT: B  245 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8035 (m-80)
REVERT: C   27 ASN cc_start: 0.8433 (t0) cc_final: 0.8115 (t0)
REVERT: C   65 ARG cc_start: 0.7408 (ttm170) cc_final: 0.6915 (ttt180)
REVERT: C  266 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8812 (mt)
REVERT: D   27 ASN cc_start: 0.8416 (t0) cc_final: 0.8055 (t0)
REVERT: D   65 ARG cc_start: 0.7367 (ttm170) cc_final: 0.6902 (ttt180)
REVERT: E   27 ASN cc_start: 0.8500 (t0) cc_final: 0.8127 (t0)
REVERT: E   65 ARG cc_start: 0.7387 (ttm170) cc_final: 0.6955 (ttt180)
REVERT: E  158 ASP cc_start: 0.6592 (m-30) cc_final: 0.6360 (m-30)
  outliers start: 33
  outliers final: 24
  residues processed: 186
  average time/residue: 0.1105
  time to fit residues: 30.4195
Evaluate side-chains
  184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  249 THR
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  191 ILE
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
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  245 TYR
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  249 THR
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  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:    4.9990
   chunk 79 optimal weight:    0.7980
   chunk 136 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0030
   chunk 90 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 148 optimal weight:    0.0570
   overall best weight:    0.5710

-------------------------------------------------------------------------------
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 = 0.3241 r_free = 0.3241 target = 0.128441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.117435 restraints weight = 15198.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.118963 restraints weight = 11707.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.119728 restraints weight = 9310.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.119975 restraints weight = 8068.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.120331 restraints weight = 7665.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12881  Z= 0.097
  Angle     :  0.488   6.637  17545  Z= 0.255
  Chirality :  0.045   0.139   1950
  Planarity :  0.004   0.052   2235
  Dihedral  :  4.307  46.657   1690
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.82 %
    Favored  : 84.22 %
  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 are not related in a simple way.
  whole:  0.04 (0.22), residues: 1525
  helix:  1.91 (0.24), residues: 475
  sheet:  0.17 (0.25), residues: 465
  loop : -1.73 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 123 
 TYR   0.008   0.001   TYR B  38 
 PHE   0.016   0.001   PHE D 282 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS E 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (12880)
  covalent geometry    : angle       0.48766 (17545)
  hydrogen bonds       : bond        0.03002 (  527)
  hydrogen bonds       : angle       4.29160 ( 1662)
  Misc. bond           : bond        0.00014 (    1)

*********************** 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
  197 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 170
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8386 (t0) cc_final: 0.8024 (t0)
REVERT: A   65 ARG cc_start: 0.7127 (ttm170) cc_final: 0.6731 (ttt180)
REVERT: A  158 ASP cc_start: 0.6179 (m-30) cc_final: 0.5964 (m-30)
REVERT: A  245 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.8160 (t80)
REVERT: B   27 ASN cc_start: 0.8396 (t0) cc_final: 0.8075 (t0)
REVERT: B   62 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: B   65 ARG cc_start: 0.7461 (ttm170) cc_final: 0.6952 (ttt180)
REVERT: B  245 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7876 (m-80)
REVERT: B  309 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (mt)
REVERT: C   27 ASN cc_start: 0.8420 (t0) cc_final: 0.8115 (t0)
REVERT: C   62 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: C  245 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8337 (t80)
REVERT: D   27 ASN cc_start: 0.8402 (t0) cc_final: 0.7990 (t0)
REVERT: D   62 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: D   65 ARG cc_start: 0.7234 (ttm170) cc_final: 0.6761 (ttt180)
REVERT: D  245 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8371 (m-80)
REVERT: E   27 ASN cc_start: 0.8472 (t0) cc_final: 0.8067 (t0)
REVERT: E   65 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6819 (ttt180)
REVERT: E  158 ASP cc_start: 0.6415 (m-30) cc_final: 0.6199 (m-30)
  outliers start: 27
  outliers final: 16
  residues processed: 183
  average time/residue: 0.1100
  time to fit residues: 29.7269
Evaluate side-chains
  175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
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  245 TYR
Chi-restraints excluded: chain A residue  249 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 B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  245 TYR
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 132 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.125708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.114923 restraints weight = 15394.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.116111 restraints weight = 11878.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.116982 restraints weight = 9741.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.117150 restraints weight = 8234.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.117321 restraints weight = 8493.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12881  Z= 0.131
  Angle     :  0.512   5.860  17545  Z= 0.270
  Chirality :  0.046   0.133   1950
  Planarity :  0.004   0.053   2235
  Dihedral  :  4.280  44.936   1690
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.98 %
    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 are not related in a simple way.
  whole:  0.05 (0.22), residues: 1525
  helix:  1.91 (0.24), residues: 475
  sheet:  0.18 (0.25), residues: 465
  loop : -1.70 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 123 
 TYR   0.012   0.001   TYR B  38 
 PHE   0.011   0.001   PHE D 282 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12880)
  covalent geometry    : angle       0.51156 (17545)
  hydrogen bonds       : bond        0.03278 (  527)
  hydrogen bonds       : angle       4.34504 ( 1662)
  Misc. bond           : bond        0.00016 (    1)

*********************** 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
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8385 (t0) cc_final: 0.8040 (t0)
REVERT: A   65 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6776 (ttt180)
REVERT: A  161 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.7112 (t60)
REVERT: B   27 ASN cc_start: 0.8382 (t0) cc_final: 0.8176 (t0)
REVERT: B   62 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: B   65 ARG cc_start: 0.7507 (ttm170) cc_final: 0.6981 (ttt180)
REVERT: B  245 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7956 (m-80)
REVERT: B  309 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: C   27 ASN cc_start: 0.8397 (t0) cc_final: 0.8126 (t0)
REVERT: C   62 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7157 (tm-30)
REVERT: C   65 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7235 (ttt180)
REVERT: D   27 ASN cc_start: 0.8377 (t0) cc_final: 0.8015 (t0)
REVERT: D   65 ARG cc_start: 0.7316 (ttm170) cc_final: 0.6842 (ttt180)
REVERT: D  245 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8487 (m-80)
REVERT: E   27 ASN cc_start: 0.8459 (t0) cc_final: 0.8076 (t0)
REVERT: E   65 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6888 (ttt180)
REVERT: E  158 ASP cc_start: 0.6475 (m-30) cc_final: 0.6244 (m-30)
REVERT: E  239 MET cc_start: 0.7382 (ttp) cc_final: 0.7029 (tmm)
  outliers start: 34
  outliers final: 21
  residues processed: 167
  average time/residue: 0.1041
  time to fit residues: 26.1648
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
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  245 TYR
Chi-restraints excluded: chain A residue  249 THR
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 B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  249 THR
Chi-restraints excluded: chain E residue   39 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  259 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0770
   chunk 67 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 117 optimal weight:    7.9990
   chunk 135 optimal weight:    0.0170
   chunk 11 optimal weight:    3.9990
   chunk 104 optimal weight:    0.3980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3230 r_free = 0.3230 target = 0.127479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.116105 restraints weight = 15291.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.117081 restraints weight = 12538.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.117368 restraints weight = 10754.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.117368 restraints weight = 9842.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.117368 restraints weight = 9841.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12881  Z= 0.109
  Angle     :  0.493   6.017  17545  Z= 0.258
  Chirality :  0.045   0.126   1950
  Planarity :  0.004   0.051   2235
  Dihedral  :  3.978  28.221   1690
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.71 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.22), residues: 1525
  helix:  1.93 (0.24), residues: 475
  sheet:  0.30 (0.25), residues: 465
  loop : -1.68 (0.24), residues: 585

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   0.009   0.001   PHE A 274 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (12880)
  covalent geometry    : angle       0.49270 (17545)
  hydrogen bonds       : bond        0.03034 (  527)
  hydrogen bonds       : angle       4.23411 ( 1662)
  Misc. bond           : bond        0.00014 (    1)

*********************** 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
  191 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8331 (t0) cc_final: 0.7938 (t0)
REVERT: A   65 ARG cc_start: 0.7199 (ttm170) cc_final: 0.6791 (ttt180)
REVERT: A  245 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8225 (t80)
REVERT: B   62 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: B   65 ARG cc_start: 0.7504 (ttm170) cc_final: 0.6950 (ttt180)
REVERT: B  245 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: B  309 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7658 (mt)
REVERT: C   27 ASN cc_start: 0.8368 (t0) cc_final: 0.8126 (t0)
REVERT: C   62 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7133 (tm-30)
REVERT: C   65 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7174 (ttt180)
REVERT: C  245 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8312 (t80)
REVERT: D   27 ASN cc_start: 0.8372 (t0) cc_final: 0.7970 (t0)
REVERT: D   62 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: D   65 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6794 (ttt180)
REVERT: D  245 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8389 (m-80)
REVERT: E   27 ASN cc_start: 0.8447 (t0) cc_final: 0.8101 (t0)
REVERT: E   65 ARG cc_start: 0.7199 (ttm170) cc_final: 0.6845 (ttt180)
REVERT: E  158 ASP cc_start: 0.6386 (m-30) cc_final: 0.6182 (m-30)
REVERT: E  239 MET cc_start: 0.7307 (ttp) cc_final: 0.6982 (tmm)
  outliers start: 30
  outliers final: 21
  residues processed: 175
  average time/residue: 0.1040
  time to fit residues: 27.4358
Evaluate side-chains
  186 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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  245 TYR
Chi-restraints excluded: chain A residue  249 THR
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 B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  249 THR
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9980
   chunk 138 optimal weight:    6.9990
   chunk 122 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 116 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3165 r_free = 0.3165 target = 0.122376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.111226 restraints weight = 15705.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.112432 restraints weight = 13695.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.113205 restraints weight = 10904.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.113694 restraints weight = 9270.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.113867 restraints weight = 8975.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12881  Z= 0.199
  Angle     :  0.574   8.264  17545  Z= 0.305
  Chirality :  0.048   0.145   1950
  Planarity :  0.004   0.053   2235
  Dihedral  :  4.576  41.491   1690
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.78 %
    Favored  : 81.75 %
  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 are not related in a simple way.
  whole: -0.13 (0.22), residues: 1525
  helix:  1.71 (0.24), residues: 475
  sheet:  0.03 (0.25), residues: 465
  loop : -1.72 (0.24), residues: 585

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   0.011   0.002   PHE E 304 
 TRP   0.017   0.001   TRP A 206 
 HIS   0.001   0.000   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (12880)
  covalent geometry    : angle       0.57410 (17545)
  hydrogen bonds       : bond        0.03836 (  527)
  hydrogen bonds       : angle       4.55300 ( 1662)
  Misc. bond           : bond        0.00024 (    1)

*********************** 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
  208 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8373 (t0) cc_final: 0.8059 (t0)
REVERT: A   65 ARG cc_start: 0.7256 (ttm170) cc_final: 0.6824 (ttt180)
REVERT: A  161 TRP cc_start: 0.7360 (OUTLIER) cc_final: 0.7134 (t60)
REVERT: B   62 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7110 (tm-30)
REVERT: B   65 ARG cc_start: 0.7552 (ttm170) cc_final: 0.6983 (ttt180)
REVERT: B  245 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8090 (m-80)
REVERT: C   27 ASN cc_start: 0.8376 (t0) cc_final: 0.8141 (t0)
REVERT: C   62 GLN cc_start: 0.7813 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: C   65 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7255 (ttt180)
REVERT: D   27 ASN cc_start: 0.8365 (t0) cc_final: 0.8029 (t0)
REVERT: D   65 ARG cc_start: 0.7380 (ttm170) cc_final: 0.6895 (ttt180)
REVERT: D  245 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8504 (m-80)
REVERT: E   27 ASN cc_start: 0.8481 (t0) cc_final: 0.8128 (t0)
REVERT: E   65 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6979 (ttt180)
REVERT: E  239 MET cc_start: 0.7424 (ttp) cc_final: 0.7136 (tmm)
  outliers start: 34
  outliers final: 27
  residues processed: 193
  average time/residue: 0.1021
  time to fit residues: 30.0617
Evaluate side-chains
  198 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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  245 TYR
Chi-restraints excluded: chain A residue  249 THR
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 B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
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  245 TYR
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  158 ASP
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  249 THR
Chi-restraints excluded: chain E residue   39 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  249 THR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  266 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0570
   chunk 2 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 140 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.127299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.116719 restraints weight = 15343.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.118520 restraints weight = 11607.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.119252 restraints weight = 9259.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.119826 restraints weight = 7854.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.119855 restraints weight = 7231.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12881  Z= 0.108
  Angle     :  0.506   6.228  17545  Z= 0.266
  Chirality :  0.045   0.127   1950
  Planarity :  0.004   0.051   2235
  Dihedral  :  4.113  46.121   1690
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.58 %
    Favored  : 81.02 %
  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 are not related in a simple way.
  whole:  0.09 (0.22), residues: 1525
  helix:  1.89 (0.24), residues: 475
  sheet:  0.19 (0.24), residues: 495
  loop : -1.72 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 123 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.020   0.001   PHE A 282 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12880)
  covalent geometry    : angle       0.50637 (17545)
  hydrogen bonds       : bond        0.03048 (  527)
  hydrogen bonds       : angle       4.23570 ( 1662)
  Misc. bond           : bond        0.00009 (    1)

********************** 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
  199 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8337 (t0) cc_final: 0.7971 (t0)
REVERT: A   65 ARG cc_start: 0.7200 (ttm170) cc_final: 0.6837 (ttt180)
REVERT: A  245 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8219 (t80)
REVERT: A  266 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8809 (mt)
REVERT: B   62 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7270 (tm-30)
REVERT: B  245 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7899 (m-80)
REVERT: C   27 ASN cc_start: 0.8344 (t0) cc_final: 0.8087 (t0)
REVERT: C   65 ARG cc_start: 0.7700 (ttm170) cc_final: 0.7261 (ttt180)
REVERT: C  245 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8308 (t80)
REVERT: D   27 ASN cc_start: 0.8334 (t0) cc_final: 0.7966 (t0)
REVERT: D   62 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7621 (tm-30)
REVERT: D   65 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6893 (ttt180)
REVERT: D  245 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (m-80)
REVERT: D  266 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8828 (mt)
REVERT: E   27 ASN cc_start: 0.8417 (t0) cc_final: 0.8066 (t0)
REVERT: E   65 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6909 (ttt180)
REVERT: E  158 ASP cc_start: 0.6397 (m-30) cc_final: 0.6184 (m-30)
REVERT: E  239 MET cc_start: 0.7263 (ttp) cc_final: 0.7020 (tmm)
  outliers start: 33
  outliers final: 25
  residues processed: 183
  average time/residue: 0.1070
  time to fit residues: 29.4915
Evaluate side-chains
  188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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  191 ILE
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  249 THR
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  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 B residue  249 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  219 SER
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  249 THR
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain E residue   39 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  259 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.3175 r_free = 0.3175 target = 0.123078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.112486 restraints weight = 15627.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.112507 restraints weight = 12414.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.112517 restraints weight = 12337.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.112517 restraints weight = 12296.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.112517 restraints weight = 12296.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12881  Z= 0.184
  Angle     :  0.564   5.249  17545  Z= 0.299
  Chirality :  0.047   0.143   1950
  Planarity :  0.004   0.053   2235
  Dihedral  :  4.513  53.164   1690
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.44 %
    Favored  : 81.09 %
  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 are not related in a simple way.
  whole: -0.08 (0.22), residues: 1525
  helix:  1.73 (0.24), residues: 475
  sheet:  0.07 (0.25), residues: 465
  loop : -1.68 (0.24), residues: 585

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   0.019   0.002   PHE A 282 
 TRP   0.017   0.001   TRP A 206 
 HIS   0.001   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (12880)
  covalent geometry    : angle       0.56402 (17545)
  hydrogen bonds       : bond        0.03679 (  527)
  hydrogen bonds       : angle       4.47452 ( 1662)
  Misc. bond           : bond        0.00027 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1626.39 seconds
wall clock time: 28 minutes 59.01 seconds (1739.01 seconds total)