Starting phenix.real_space_refine
on Thu Sep 18 00:35:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngc_49382/09_2025/9ngc_49382_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngc_49382/09_2025/9ngc_49382.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngc_49382/09_2025/9ngc_49382.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngc_49382/09_2025/9ngc_49382.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ngc_49382/09_2025/9ngc_49382_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngc_49382/09_2025/9ngc_49382_neut.cif"
  }
  resolution = 2.8
  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=   0.131
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      25      5.16       5
     Na      2      4.78       5
     C    8305      2.51       5
     N    2115      2.21       5
     O    2275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12722
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2540
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 13, 'TRANS': 296}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 6
          Unusual residues: {' NA': 2, '3CN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.94, per 1000 atoms: 0.15
  Number of scatterers: 12722
  At special positions: 0
  Unit cell: (91.14, 93.744, 124.992, 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      25     16.00
     Na      2     11.00
     O    2275      8.00
     N    2115      7.00
     C    8305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 627.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2930

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 20 sheets defined
      36.8% alpha, 41.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.842A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG A 301 " --> pdb=" O   GLN A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 301'
    Processing helix  chain 'A' and resid 302 through 320
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.842A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'B' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG B 301 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 301'
    Processing helix  chain 'B' and resid 302 through 320
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.842A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'C' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER C 235 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE C 252 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG C 301 " --> pdb=" O   GLN C 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 298 through 301'
    Processing helix  chain 'C' and resid 302 through 320
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.843A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing helix  chain 'D' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR D 234 " --> pdb=" O   GLU D 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER D 235 " --> pdb=" O   ARG D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 253
      removed outlier: 3.634A  pdb=" N   ASN D 251 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE D 252 " --> pdb=" O   TYR D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG D 301 " --> pdb=" O   GLN D 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 298 through 301'
    Processing helix  chain 'D' and resid 302 through 320
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.843A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 222
    Processing helix  chain 'E' and resid 223 through 225
      No H-bonds generated for 'chain 'E' and resid 223 through 225'
    Processing helix  chain 'E' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR E 234 " --> pdb=" O   GLU E 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER E 235 " --> pdb=" O   ARG E 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN E 251 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE E 252 " --> pdb=" O   TYR E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG E 301 " --> pdb=" O   GLN E 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 298 through 301'
    Processing helix  chain 'E' and resid 302 through 320
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.364A  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: 3.574A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.363A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.575A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    690 hydrogen bonds defined for protein.
    1995 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.26 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: 3688
        1.34 -     1.45: 2308
        1.45 -     1.57: 7019
        1.57 -     1.69: 5
        1.69 -     1.80: 45
  Bond restraints: 13065
  Sorted by residual:
  bond pdb=" C   PHE D 304 "
       pdb=" N   PRO D 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.18e+00
  bond pdb=" C   PHE E 304 "
       pdb=" N   PRO E 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.17e+00
  bond pdb=" C   PHE A 304 "
       pdb=" N   PRO A 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.15e+00
  bond pdb=" C   PHE B 304 "
       pdb=" N   PRO B 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.13e+00
  bond pdb=" C   PHE C 304 "
       pdb=" N   PRO C 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.018 1.23e-02 6.61e+03 2.11e+00
  ... (remaining 13060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 17044
        1.53 -     3.05: 576
        3.05 -     4.58: 95
        4.58 -     6.11: 35
        6.11 -     7.63: 30
  Bond angle restraints: 17780
  Sorted by residual:
  angle pdb=" C   ASN B  60 "
        pdb=" N   THR B  61 "
        pdb=" CA  THR B  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.17   -7.63 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   ASN A  60 "
        pdb=" N   THR A  61 "
        pdb=" CA  THR A  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.12   -7.58 1.91e+00 2.74e-01 1.57e+01
  angle pdb=" C   ASN C  60 "
        pdb=" N   THR C  61 "
        pdb=" CA  THR C  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.11   -7.57 1.91e+00 2.74e-01 1.57e+01
  angle pdb=" C   ASN E  60 "
        pdb=" N   THR E  61 "
        pdb=" CA  THR E  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" C   ASN D  60 "
        pdb=" N   THR D  61 "
        pdb=" CA  THR D  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.08   -7.54 1.91e+00 2.74e-01 1.56e+01
  ... (remaining 17775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.15: 6517
       12.15 -    24.29: 808
       24.29 -    36.44: 210
       36.44 -    48.59: 60
       48.59 -    60.73: 10
  Dihedral angle restraints: 7605
    sinusoidal: 3060
      harmonic: 4545
  Sorted by residual:
  dihedral pdb=" CA  ILE D 157 "
           pdb=" C   ILE D 157 "
           pdb=" N   ASP D 158 "
           pdb=" CA  ASP D 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.94  -23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  ILE A 157 "
           pdb=" C   ILE A 157 "
           pdb=" N   ASP A 158 "
           pdb=" CA  ASP A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  ILE C 157 "
           pdb=" C   ILE C 157 "
           pdb=" N   ASP C 158 "
           pdb=" CA  ASP C 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 7602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1428
       0.049 -    0.097: 373
       0.097 -    0.146: 134
       0.146 -    0.194: 15
       0.194 -    0.243: 5
  Chirality restraints: 1955
  Sorted by residual:
  chirality pdb=" CB  THR B 149 "
            pdb=" CA  THR B 149 "
            pdb=" OG1 THR B 149 "
            pdb=" CG2 THR B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  THR A 149 "
            pdb=" CA  THR A 149 "
            pdb=" OG1 THR A 149 "
            pdb=" CG2 THR A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CB  THR E 149 "
            pdb=" CA  THR E 149 "
            pdb=" OG1 THR E 149 "
            pdb=" CG2 THR E 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1952 not shown)

  Planarity restraints: 2265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  54 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.04e+00
        pdb=" N   PRO B  55 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B  55 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  55 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  54 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO A  55 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  55 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  55 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E  54 "    0.033 5.00e-02 4.00e+02   5.02e-02 4.02e+00
        pdb=" N   PRO E  55 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO E  55 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E  55 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2262 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1811
        2.76 -     3.30: 11025
        3.30 -     3.83: 20891
        3.83 -     4.37: 24391
        4.37 -     4.90: 43952
  Nonbonded interactions: 102070
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 229 "
            pdb=" OE2 GLU E 230 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER C 229 "
            pdb=" OE2 GLU D 230 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER A 229 "
            pdb=" OE2 GLU B 230 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE2 GLU A 230 "
            pdb=" OG  SER E 229 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER B 229 "
            pdb=" OE2 GLU C 230 "
     model   vdw
     2.265 3.040
  ... (remaining 102065 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'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.800
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.010
  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:6.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
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      :  0.004   0.041  13065  Z= 0.185
  Angle     :  0.728   7.632  17780  Z= 0.381
  Chirality :  0.050   0.243   1955
  Planarity :  0.005   0.050   2265
  Dihedral  : 11.953  60.734   4675
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.21), residues: 1540
  helix: -0.60 (0.20), residues: 565
  sheet:  1.40 (0.25), residues: 465
  loop : -2.16 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  91 
 TYR   0.009   0.001   TYR B 203 
 PHE   0.011   0.002   PHE E 116 
 TRP   0.020   0.002   TRP C 206 
 HIS   0.004   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (13065)
  covalent geometry    : angle       0.72810 (17780)
  hydrogen bonds       : bond        0.15258 (  600)
  hydrogen bonds       : angle       6.85309 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8021 (t0) cc_final: 0.7726 (t70)
REVERT: A  155 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6675 (mm-30)
REVERT: A  176 ASP cc_start: 0.7778 (m-30) cc_final: 0.7555 (m-30)
REVERT: A  187 GLU cc_start: 0.7446 (tt0) cc_final: 0.7181 (tt0)
REVERT: B   34 LYS cc_start: 0.8301 (mttm) cc_final: 0.8091 (mttp)
REVERT: B   36 ASP cc_start: 0.8020 (t0) cc_final: 0.7656 (t70)
REVERT: B   61 THR cc_start: 0.8208 (t) cc_final: 0.7807 (p)
REVERT: B   69 ASN cc_start: 0.7815 (m-40) cc_final: 0.7601 (m-40)
REVERT: B   90 LYS cc_start: 0.8336 (pttt) cc_final: 0.7839 (ptpp)
REVERT: B  155 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6692 (mm-30)
REVERT: C   27 ASN cc_start: 0.8271 (t0) cc_final: 0.8044 (t0)
REVERT: C   36 ASP cc_start: 0.8036 (t0) cc_final: 0.7614 (t0)
REVERT: C   61 THR cc_start: 0.8176 (t) cc_final: 0.7742 (p)
REVERT: C   90 LYS cc_start: 0.8308 (pttt) cc_final: 0.7826 (ptpp)
REVERT: C  155 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6665 (mm-30)
REVERT: C  187 GLU cc_start: 0.7660 (tt0) cc_final: 0.7405 (tt0)
REVERT: C  233 GLN cc_start: 0.6719 (pt0) cc_final: 0.6490 (pt0)
REVERT: D   34 LYS cc_start: 0.8255 (mttm) cc_final: 0.8024 (mttp)
REVERT: D   36 ASP cc_start: 0.8108 (t0) cc_final: 0.7886 (t70)
REVERT: D   90 LYS cc_start: 0.8440 (pttt) cc_final: 0.7937 (ptpp)
REVERT: D  150 GLU cc_start: 0.7664 (pm20) cc_final: 0.7405 (mp0)
REVERT: D  155 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6711 (mm-30)
REVERT: D  176 ASP cc_start: 0.7708 (m-30) cc_final: 0.7425 (m-30)
REVERT: D  233 GLN cc_start: 0.6844 (pt0) cc_final: 0.6618 (pt0)
REVERT: E   36 ASP cc_start: 0.7960 (t0) cc_final: 0.7660 (t70)
REVERT: E   61 THR cc_start: 0.8127 (t) cc_final: 0.7689 (p)
REVERT: E  155 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6632 (mm-30)
REVERT: E  233 GLN cc_start: 0.7002 (pt0) cc_final: 0.6725 (pt0)
REVERT: E  239 MET cc_start: 0.7824 (ttp) cc_final: 0.7565 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.7087
  time to fit residues: 144.1764
Evaluate side-chains
  140 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 146 GLN
A 184 ASN
B  27 ASN
B  42 GLN
B 146 GLN
C  42 GLN
D  42 GLN
E  27 ASN
E  42 GLN
E 146 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.152543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.119460 restraints weight = 14346.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.18
r_work: 0.3341 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13065  Z= 0.147
  Angle     :  0.544   5.619  17780  Z= 0.287
  Chirality :  0.045   0.137   1955
  Planarity :  0.004   0.043   2265
  Dihedral  :  4.496  19.402   1715
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  7.15 %
    Favored  : 91.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.22), residues: 1540
  helix:  0.73 (0.23), residues: 530
  sheet:  1.33 (0.25), residues: 470
  loop : -2.06 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  91 
 TYR   0.008   0.001   TYR A 204 
 PHE   0.010   0.001   PHE C 304 
 TRP   0.014   0.001   TRP B 206 
 HIS   0.004   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (13065)
  covalent geometry    : angle       0.54408 (17780)
  hydrogen bonds       : bond        0.03626 (  600)
  hydrogen bonds       : angle       4.68681 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A  150 GLU cc_start: 0.7775 (pm20) cc_final: 0.7443 (mp0)
REVERT: A  155 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6846 (mm-30)
REVERT: A  156 GLU cc_start: 0.7755 (tt0) cc_final: 0.7414 (tt0)
REVERT: A  176 ASP cc_start: 0.7963 (m-30) cc_final: 0.7631 (m-30)
REVERT: A  187 GLU cc_start: 0.7606 (tt0) cc_final: 0.7378 (mt-10)
REVERT: B   27 ASN cc_start: 0.8251 (t0) cc_final: 0.7847 (t0)
REVERT: B   90 LYS cc_start: 0.8351 (pttt) cc_final: 0.7899 (ptpp)
REVERT: B   93 MET cc_start: 0.8672 (ttm) cc_final: 0.8244 (mtp)
REVERT: B  150 GLU cc_start: 0.7784 (pm20) cc_final: 0.7259 (mp0)
REVERT: B  155 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6553 (mm-30)
REVERT: B  156 GLU cc_start: 0.7690 (tt0) cc_final: 0.7341 (tt0)
REVERT: C   27 ASN cc_start: 0.8234 (t0) cc_final: 0.7987 (t0)
REVERT: C   90 LYS cc_start: 0.8277 (pttt) cc_final: 0.7731 (ptpp)
REVERT: C  150 GLU cc_start: 0.7702 (pm20) cc_final: 0.7312 (mp0)
REVERT: C  155 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6845 (mm-30)
REVERT: D   27 ASN cc_start: 0.8080 (t0) cc_final: 0.7323 (t0)
REVERT: D   34 LYS cc_start: 0.8324 (mttm) cc_final: 0.8124 (mmtp)
REVERT: D   90 LYS cc_start: 0.8416 (pttt) cc_final: 0.7819 (ptpp)
REVERT: D   93 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8308 (mtp)
REVERT: D  150 GLU cc_start: 0.7627 (pm20) cc_final: 0.7245 (mp0)
REVERT: D  155 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6884 (mm-30)
REVERT: D  176 ASP cc_start: 0.7896 (m-30) cc_final: 0.7532 (m-30)
REVERT: D  233 GLN cc_start: 0.6597 (pt0) cc_final: 0.6350 (tt0)
REVERT: E   93 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8313 (mtp)
REVERT: E  155 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6886 (mm-30)
REVERT: E  174 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7640 (ttm-80)
REVERT: E  239 MET cc_start: 0.7667 (ttp) cc_final: 0.7461 (ttp)
  outliers start: 19
  outliers final: 6
  residues processed: 170
  average time/residue: 0.7678
  time to fit residues: 139.5019
Evaluate side-chains
  160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 184 ASN
A 233 GLN
B  42 GLN
C  42 GLN
D  42 GLN
E  27 ASN
E  42 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116070 restraints weight = 14422.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.15
r_work: 0.3303 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027  13065  Z= 0.197
  Angle     :  0.570   6.493  17780  Z= 0.301
  Chirality :  0.047   0.139   1955
  Planarity :  0.004   0.043   2265
  Dihedral  :  4.607  20.022   1715
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.68 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.22), residues: 1540
  helix:  0.77 (0.23), residues: 560
  sheet:  1.46 (0.27), residues: 435
  loop : -2.07 (0.23), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  91 
 TYR   0.009   0.001   TYR E 148 
 PHE   0.012   0.001   PHE C 116 
 TRP   0.021   0.001   TRP C 206 
 HIS   0.005   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (13065)
  covalent geometry    : angle       0.57002 (17780)
  hydrogen bonds       : bond        0.03775 (  600)
  hydrogen bonds       : angle       4.64030 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A   69 ASN cc_start: 0.7624 (m-40) cc_final: 0.7385 (m-40)
REVERT: A  150 GLU cc_start: 0.7884 (pm20) cc_final: 0.7432 (mp0)
REVERT: A  155 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6859 (mm-30)
REVERT: A  156 GLU cc_start: 0.7783 (tt0) cc_final: 0.7418 (tt0)
REVERT: A  163 ARG cc_start: 0.7411 (mmt90) cc_final: 0.7132 (mmt90)
REVERT: A  176 ASP cc_start: 0.8126 (m-30) cc_final: 0.7819 (m-30)
REVERT: A  187 GLU cc_start: 0.7707 (tt0) cc_final: 0.7395 (mt-10)
REVERT: B   27 ASN cc_start: 0.8209 (t0) cc_final: 0.7757 (t0)
REVERT: B   90 LYS cc_start: 0.8392 (pttt) cc_final: 0.7910 (ptpp)
REVERT: B  155 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6937 (mm-30)
REVERT: B  163 ARG cc_start: 0.7431 (mmt90) cc_final: 0.7098 (mmp80)
REVERT: C   29 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7730 (tt)
REVERT: C   34 LYS cc_start: 0.8486 (mttm) cc_final: 0.8129 (mttm)
REVERT: C   36 ASP cc_start: 0.8903 (t0) cc_final: 0.8611 (t70)
REVERT: C   90 LYS cc_start: 0.8283 (pttt) cc_final: 0.7743 (ptpp)
REVERT: C  150 GLU cc_start: 0.7807 (pm20) cc_final: 0.7370 (mp0)
REVERT: C  155 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6872 (mm-30)
REVERT: C  159 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6977 (pt0)
REVERT: C  163 ARG cc_start: 0.7491 (mmt90) cc_final: 0.7167 (mmt90)
REVERT: D   34 LYS cc_start: 0.8355 (mttm) cc_final: 0.8135 (mmtp)
REVERT: D   90 LYS cc_start: 0.8381 (pttt) cc_final: 0.7823 (ptpp)
REVERT: D   93 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8326 (mtp)
REVERT: D  155 GLU cc_start: 0.7708 (mt-10) cc_final: 0.6956 (mm-30)
REVERT: D  159 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7141 (pt0)
REVERT: D  163 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7191 (mmp80)
REVERT: D  176 ASP cc_start: 0.7935 (m-30) cc_final: 0.7607 (m-30)
REVERT: E   36 ASP cc_start: 0.8870 (t0) cc_final: 0.8598 (t70)
REVERT: E   93 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8341 (mtp)
REVERT: E  150 GLU cc_start: 0.7925 (pm20) cc_final: 0.7443 (mp0)
REVERT: E  155 GLU cc_start: 0.7636 (mt-10) cc_final: 0.6998 (mm-30)
REVERT: E  156 GLU cc_start: 0.7698 (tt0) cc_final: 0.7308 (tt0)
REVERT: E  163 ARG cc_start: 0.7404 (mmt90) cc_final: 0.7105 (mmt90)
REVERT: E  185 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7322 (pt0)
  outliers start: 18
  outliers final: 6
  residues processed: 173
  average time/residue: 0.7930
  time to fit residues: 146.8051
Evaluate side-chains
  162 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  159 GLU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  159 GLU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 142 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 90 optimal weight:    0.0870
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
A 184 ASN
A 233 GLN
D  27 ASN
E  27 ASN
E 233 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.153075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.120070 restraints weight = 14402.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.17
r_work: 0.3360 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13065  Z= 0.100
  Angle     :  0.476   5.224  17780  Z= 0.248
  Chirality :  0.044   0.142   1955
  Planarity :  0.003   0.042   2265
  Dihedral  :  4.182  18.448   1715
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.62 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.22), residues: 1540
  helix:  1.35 (0.23), residues: 530
  sheet:  1.50 (0.26), residues: 470
  loop : -2.01 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 163 
 TYR   0.005   0.001   TYR B 203 
 PHE   0.008   0.001   PHE D 116 
 TRP   0.024   0.001   TRP C 206 
 HIS   0.002   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (13065)
  covalent geometry    : angle       0.47565 (17780)
  hydrogen bonds       : bond        0.02797 (  600)
  hydrogen bonds       : angle       4.24753 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  150 GLU cc_start: 0.7795 (pm20) cc_final: 0.7408 (mp0)
REVERT: A  155 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6759 (mm-30)
REVERT: A  156 GLU cc_start: 0.7767 (tt0) cc_final: 0.7343 (tt0)
REVERT: A  176 ASP cc_start: 0.8008 (m-30) cc_final: 0.7621 (m-30)
REVERT: B   27 ASN cc_start: 0.7867 (t0) cc_final: 0.7566 (t0)
REVERT: B   69 ASN cc_start: 0.7466 (m-40) cc_final: 0.7185 (m-40)
REVERT: B   90 LYS cc_start: 0.8349 (pttt) cc_final: 0.7841 (ptpp)
REVERT: B   93 MET cc_start: 0.8583 (ttm) cc_final: 0.8179 (mtp)
REVERT: B  137 ASN cc_start: 0.7350 (p0) cc_final: 0.7054 (p0)
REVERT: B  150 GLU cc_start: 0.7738 (pm20) cc_final: 0.7151 (mp0)
REVERT: B  155 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6716 (mm-30)
REVERT: B  156 GLU cc_start: 0.7717 (tt0) cc_final: 0.7275 (tt0)
REVERT: B  163 ARG cc_start: 0.7385 (mmt90) cc_final: 0.7081 (mmp80)
REVERT: C   27 ASN cc_start: 0.8243 (t0) cc_final: 0.7964 (t0)
REVERT: C   29 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7636 (tt)
REVERT: C   90 LYS cc_start: 0.8190 (pttt) cc_final: 0.7595 (ptpp)
REVERT: C   93 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8284 (mtp)
REVERT: C  137 ASN cc_start: 0.7367 (p0) cc_final: 0.7130 (p0)
REVERT: C  150 GLU cc_start: 0.7656 (pm20) cc_final: 0.7268 (mp0)
REVERT: C  155 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6782 (mm-30)
REVERT: C  163 ARG cc_start: 0.7361 (mmt90) cc_final: 0.7099 (mmt90)
REVERT: D   34 LYS cc_start: 0.8300 (mttm) cc_final: 0.8008 (mmtp)
REVERT: D   69 ASN cc_start: 0.7469 (m-40) cc_final: 0.7237 (m-40)
REVERT: D   90 LYS cc_start: 0.8260 (pttt) cc_final: 0.7762 (ptpp)
REVERT: D   93 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8312 (mtp)
REVERT: D  137 ASN cc_start: 0.7517 (p0) cc_final: 0.7188 (p0)
REVERT: D  150 GLU cc_start: 0.7644 (pm20) cc_final: 0.7198 (mp0)
REVERT: D  155 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6785 (mm-30)
REVERT: D  163 ARG cc_start: 0.7383 (mmt90) cc_final: 0.7167 (mmp80)
REVERT: D  187 GLU cc_start: 0.7509 (tt0) cc_final: 0.7231 (mt-10)
REVERT: E   93 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8395 (mtp)
REVERT: E  155 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6866 (mm-30)
REVERT: E  163 ARG cc_start: 0.7333 (mmt90) cc_final: 0.7098 (mmp80)
REVERT: E  185 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7305 (pt0)
  outliers start: 17
  outliers final: 9
  residues processed: 175
  average time/residue: 0.7075
  time to fit residues: 132.7809
Evaluate side-chains
  175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  159 GLU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 7 optimal weight:    0.0770
   chunk 43 optimal weight:    0.9980
   chunk 135 optimal weight:    4.9990
   chunk 140 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 106 optimal weight:    0.1980
   chunk 79 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 6 optimal weight:    0.3980
   chunk 122 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.155315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.122616 restraints weight = 14395.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.16
r_work: 0.3386 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13065  Z= 0.090
  Angle     :  0.458   5.149  17780  Z= 0.238
  Chirality :  0.043   0.141   1955
  Planarity :  0.003   0.041   2265
  Dihedral  :  3.875  17.425   1715
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.99 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.23), residues: 1540
  helix:  1.57 (0.23), residues: 530
  sheet:  1.65 (0.27), residues: 465
  loop : -1.92 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 163 
 TYR   0.005   0.001   TYR B 203 
 PHE   0.008   0.001   PHE C 116 
 TRP   0.023   0.001   TRP C 206 
 HIS   0.002   0.000   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 (13065)
  covalent geometry    : angle       0.45840 (17780)
  hydrogen bonds       : bond        0.02564 (  600)
  hydrogen bonds       : angle       4.00375 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A   93 MET cc_start: 0.8439 (mtp) cc_final: 0.8227 (mmm)
REVERT: A  150 GLU cc_start: 0.7785 (pm20) cc_final: 0.7469 (mp0)
REVERT: A  155 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6794 (mm-30)
REVERT: A  156 GLU cc_start: 0.7890 (tt0) cc_final: 0.7525 (tt0)
REVERT: A  163 ARG cc_start: 0.7188 (mmt90) cc_final: 0.6946 (mmp80)
REVERT: B   27 ASN cc_start: 0.7807 (t0) cc_final: 0.7471 (t0)
REVERT: B   69 ASN cc_start: 0.7476 (m-40) cc_final: 0.7220 (m-40)
REVERT: B   90 LYS cc_start: 0.8371 (pttt) cc_final: 0.7807 (ptpp)
REVERT: B   93 MET cc_start: 0.8599 (ttm) cc_final: 0.8217 (mtp)
REVERT: B  150 GLU cc_start: 0.7745 (pm20) cc_final: 0.7246 (mp0)
REVERT: B  155 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6687 (mm-30)
REVERT: B  156 GLU cc_start: 0.7740 (tt0) cc_final: 0.7373 (tt0)
REVERT: B  163 ARG cc_start: 0.7316 (mmt90) cc_final: 0.6964 (mmp80)
REVERT: C   27 ASN cc_start: 0.8234 (t0) cc_final: 0.7966 (t0)
REVERT: C   29 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7721 (tt)
REVERT: C   34 LYS cc_start: 0.8395 (mttm) cc_final: 0.7987 (mttm)
REVERT: C   90 LYS cc_start: 0.8219 (pttt) cc_final: 0.7710 (ptpp)
REVERT: C   93 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (mtp)
REVERT: C  150 GLU cc_start: 0.7725 (pm20) cc_final: 0.7325 (mp0)
REVERT: C  155 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6688 (mm-30)
REVERT: C  163 ARG cc_start: 0.7239 (mmt90) cc_final: 0.7027 (mmp80)
REVERT: D   27 ASN cc_start: 0.7875 (t0) cc_final: 0.7287 (t0)
REVERT: D   34 LYS cc_start: 0.8338 (mttm) cc_final: 0.8050 (mmtp)
REVERT: D   90 LYS cc_start: 0.8290 (pttt) cc_final: 0.7785 (ptpp)
REVERT: D  137 ASN cc_start: 0.7372 (p0) cc_final: 0.7037 (p0)
REVERT: D  150 GLU cc_start: 0.7693 (pm20) cc_final: 0.7207 (mp0)
REVERT: D  155 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6844 (mm-30)
REVERT: D  159 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6745 (pt0)
REVERT: D  163 ARG cc_start: 0.7292 (mmt90) cc_final: 0.7038 (mmp80)
REVERT: D  187 GLU cc_start: 0.7550 (tt0) cc_final: 0.7290 (mt-10)
REVERT: E   93 MET cc_start: 0.8646 (ttp) cc_final: 0.8402 (mtp)
REVERT: E  150 GLU cc_start: 0.7785 (pm20) cc_final: 0.7322 (mp0)
REVERT: E  155 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6708 (mm-30)
REVERT: E  156 GLU cc_start: 0.7718 (tt0) cc_final: 0.7377 (tt0)
REVERT: E  163 ARG cc_start: 0.7341 (mmt90) cc_final: 0.7117 (mmp80)
REVERT: E  185 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7408 (pt0)
  outliers start: 23
  outliers final: 7
  residues processed: 182
  average time/residue: 0.7192
  time to fit residues: 140.6663
Evaluate side-chains
  169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  159 GLU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  159 GLU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 152 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 33 optimal weight:    0.3980
   chunk 129 optimal weight:    4.9990
   chunk 143 optimal weight:    0.0980
   chunk 60 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
D  21 ASN
E  21 ASN
E 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.146732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.114539 restraints weight = 14326.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.12
r_work: 0.3297 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  13065  Z= 0.213
  Angle     :  0.567   6.671  17780  Z= 0.298
  Chirality :  0.047   0.140   1955
  Planarity :  0.004   0.042   2265
  Dihedral  :  4.402  19.744   1715
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.07 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.23), residues: 1540
  helix:  1.44 (0.23), residues: 530
  sheet:  1.39 (0.27), residues: 465
  loop : -1.95 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 117 
 TYR   0.009   0.001   TYR E 204 
 PHE   0.013   0.001   PHE E 116 
 TRP   0.025   0.002   TRP C 206 
 HIS   0.006   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (13065)
  covalent geometry    : angle       0.56673 (17780)
  hydrogen bonds       : bond        0.03544 (  600)
  hydrogen bonds       : angle       4.43809 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A   69 ASN cc_start: 0.7583 (m-40) cc_final: 0.7377 (m-40)
REVERT: A  150 GLU cc_start: 0.7849 (pm20) cc_final: 0.7481 (mp0)
REVERT: A  155 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6903 (mm-30)
REVERT: A  156 GLU cc_start: 0.7763 (tt0) cc_final: 0.7349 (tt0)
REVERT: B   36 ASP cc_start: 0.8978 (t0) cc_final: 0.8745 (t70)
REVERT: B   69 ASN cc_start: 0.7553 (m-40) cc_final: 0.7279 (m-40)
REVERT: B   90 LYS cc_start: 0.8404 (pttt) cc_final: 0.7889 (ptpp)
REVERT: B   93 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8208 (mtp)
REVERT: B  155 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6738 (mm-30)
REVERT: C   29 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7692 (tt)
REVERT: C   36 ASP cc_start: 0.8931 (t0) cc_final: 0.8668 (t70)
REVERT: C   90 LYS cc_start: 0.8239 (pttt) cc_final: 0.7664 (ptpp)
REVERT: C  150 GLU cc_start: 0.7891 (pm20) cc_final: 0.7358 (mp0)
REVERT: C  155 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6732 (mm-30)
REVERT: D   34 LYS cc_start: 0.8346 (mttm) cc_final: 0.8101 (mmtp)
REVERT: D   36 ASP cc_start: 0.8825 (t0) cc_final: 0.8539 (t70)
REVERT: D   69 ASN cc_start: 0.7503 (m-40) cc_final: 0.7247 (m-40)
REVERT: D   86 ASP cc_start: 0.7723 (t70) cc_final: 0.7462 (t0)
REVERT: D   90 LYS cc_start: 0.8333 (pttt) cc_final: 0.7832 (ptpp)
REVERT: D  129 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8396 (mt-10)
REVERT: D  137 ASN cc_start: 0.7717 (p0) cc_final: 0.7345 (p0)
REVERT: D  155 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6861 (mm-30)
REVERT: D  187 GLU cc_start: 0.7486 (tt0) cc_final: 0.7170 (mt-10)
REVERT: E   36 ASP cc_start: 0.8874 (t0) cc_final: 0.8548 (t70)
REVERT: E  150 GLU cc_start: 0.7956 (pm20) cc_final: 0.7482 (mp0)
REVERT: E  155 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6908 (mm-30)
REVERT: E  156 GLU cc_start: 0.7761 (tt0) cc_final: 0.7373 (tt0)
REVERT: E  163 ARG cc_start: 0.7314 (mmt90) cc_final: 0.7065 (mmp80)
REVERT: E  185 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7370 (pt0)
  outliers start: 35
  outliers final: 18
  residues processed: 170
  average time/residue: 0.7250
  time to fit residues: 132.3548
Evaluate side-chains
  166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 120 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 152 optimal weight:    0.2980
   chunk 69 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.154162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.120778 restraints weight = 14459.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.14
r_work: 0.3359 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13065  Z= 0.105
  Angle     :  0.478   5.289  17780  Z= 0.250
  Chirality :  0.044   0.135   1955
  Planarity :  0.003   0.043   2265
  Dihedral  :  4.060  18.302   1715
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.58 %
    Favored  : 83.75 %
  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 aren not related in a simple way.
  whole:  0.62 (0.23), residues: 1540
  helix:  1.60 (0.23), residues: 530
  sheet:  1.55 (0.27), residues: 465
  loop : -1.94 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 163 
 TYR   0.006   0.001   TYR B 203 
 PHE   0.009   0.001   PHE B 116 
 TRP   0.025   0.001   TRP C 206 
 HIS   0.002   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (13065)
  covalent geometry    : angle       0.47836 (17780)
  hydrogen bonds       : bond        0.02737 (  600)
  hydrogen bonds       : angle       4.16789 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  150 GLU cc_start: 0.7830 (pm20) cc_final: 0.7460 (mp0)
REVERT: A  155 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6865 (mm-30)
REVERT: A  156 GLU cc_start: 0.7867 (tt0) cc_final: 0.7514 (tt0)
REVERT: A  163 ARG cc_start: 0.7262 (mmt90) cc_final: 0.7061 (mmp80)
REVERT: B   27 ASN cc_start: 0.8148 (t0) cc_final: 0.7793 (t0)
REVERT: B   90 LYS cc_start: 0.8405 (pttt) cc_final: 0.7900 (ptpp)
REVERT: B   93 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8190 (mtp)
REVERT: B  137 ASN cc_start: 0.7689 (p0) cc_final: 0.7410 (p0)
REVERT: B  150 GLU cc_start: 0.7751 (pm20) cc_final: 0.7186 (mp0)
REVERT: B  155 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6696 (mm-30)
REVERT: B  156 GLU cc_start: 0.7827 (tt0) cc_final: 0.7446 (tt0)
REVERT: B  163 ARG cc_start: 0.7423 (mmp80) cc_final: 0.7187 (mmp80)
REVERT: B  174 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7529 (ttm-80)
REVERT: C   29 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7800 (tt)
REVERT: C   90 LYS cc_start: 0.8237 (pttt) cc_final: 0.7739 (ptpp)
REVERT: C   93 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8336 (mtp)
REVERT: C  150 GLU cc_start: 0.7822 (pm20) cc_final: 0.7320 (mp0)
REVERT: C  155 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6785 (mm-30)
REVERT: D   27 ASN cc_start: 0.7939 (t0) cc_final: 0.7366 (t0)
REVERT: D   30 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7309 (mt-10)
REVERT: D   34 LYS cc_start: 0.8313 (mttm) cc_final: 0.8056 (mttp)
REVERT: D   69 ASN cc_start: 0.7472 (m-40) cc_final: 0.7223 (m-40)
REVERT: D   86 ASP cc_start: 0.7687 (t70) cc_final: 0.7439 (t0)
REVERT: D   90 LYS cc_start: 0.8320 (pttt) cc_final: 0.7821 (ptpp)
REVERT: D  137 ASN cc_start: 0.7533 (p0) cc_final: 0.7166 (p0)
REVERT: D  150 GLU cc_start: 0.7830 (pm20) cc_final: 0.7248 (mt-10)
REVERT: D  155 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6910 (mm-30)
REVERT: D  156 GLU cc_start: 0.7740 (tt0) cc_final: 0.7127 (tp30)
REVERT: D  187 GLU cc_start: 0.7533 (tt0) cc_final: 0.7260 (mt-10)
REVERT: E  155 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6885 (mm-30)
REVERT: E  185 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7446 (pt0)
  outliers start: 23
  outliers final: 11
  residues processed: 159
  average time/residue: 0.7585
  time to fit residues: 129.1005
Evaluate side-chains
  160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 126 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0470
   chunk 74 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   chunk 86 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
C  27 ASN
E 233 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.148015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.115797 restraints weight = 14257.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.13
r_work: 0.3317 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  13065  Z= 0.163
  Angle     :  0.524   5.468  17780  Z= 0.275
  Chirality :  0.045   0.132   1955
  Planarity :  0.004   0.042   2265
  Dihedral  :  4.250  19.007   1715
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.73 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.23), residues: 1540
  helix:  1.57 (0.23), residues: 530
  sheet:  1.67 (0.27), residues: 435
  loop : -1.98 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 163 
 TYR   0.007   0.001   TYR E 204 
 PHE   0.011   0.001   PHE D 116 
 TRP   0.029   0.002   TRP C 206 
 HIS   0.004   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (13065)
  covalent geometry    : angle       0.52360 (17780)
  hydrogen bonds       : bond        0.03173 (  600)
  hydrogen bonds       : angle       4.32252 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   69 ASN cc_start: 0.7532 (m-40) cc_final: 0.7326 (m-40)
REVERT: A  124 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.6456 (mp10)
REVERT: A  150 GLU cc_start: 0.7841 (pm20) cc_final: 0.7431 (mp0)
REVERT: A  155 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6858 (mm-30)
REVERT: A  156 GLU cc_start: 0.7724 (tt0) cc_final: 0.7298 (tt0)
REVERT: A  163 ARG cc_start: 0.7325 (mmt90) cc_final: 0.7067 (mmp80)
REVERT: B   36 ASP cc_start: 0.8996 (t0) cc_final: 0.8546 (t70)
REVERT: B   90 LYS cc_start: 0.8383 (pttt) cc_final: 0.7860 (ptpp)
REVERT: B   93 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8151 (mtp)
REVERT: B  137 ASN cc_start: 0.7779 (p0) cc_final: 0.7526 (p0)
REVERT: B  155 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6715 (mm-30)
REVERT: B  174 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7568 (ttm-80)
REVERT: C   29 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7673 (tt)
REVERT: C   36 ASP cc_start: 0.8928 (t0) cc_final: 0.8533 (t70)
REVERT: C   90 LYS cc_start: 0.8207 (pttt) cc_final: 0.7631 (ptpp)
REVERT: C  150 GLU cc_start: 0.7844 (pm20) cc_final: 0.7311 (mp0)
REVERT: C  155 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6749 (mm-30)
REVERT: C  163 ARG cc_start: 0.7176 (mmt90) cc_final: 0.6956 (mmt90)
REVERT: D   34 LYS cc_start: 0.8336 (mttm) cc_final: 0.8095 (mttp)
REVERT: D   69 ASN cc_start: 0.7442 (m-40) cc_final: 0.7202 (m-40)
REVERT: D   86 ASP cc_start: 0.7692 (t70) cc_final: 0.7418 (t0)
REVERT: D   90 LYS cc_start: 0.8280 (pttt) cc_final: 0.7774 (ptpp)
REVERT: D  137 ASN cc_start: 0.7637 (p0) cc_final: 0.7246 (p0)
REVERT: D  155 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6826 (mm-30)
REVERT: D  174 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7670 (ttm-80)
REVERT: D  187 GLU cc_start: 0.7448 (tt0) cc_final: 0.7144 (mt-10)
REVERT: E   36 ASP cc_start: 0.8832 (t0) cc_final: 0.8481 (t70)
REVERT: E  150 GLU cc_start: 0.7884 (pm20) cc_final: 0.7385 (mp0)
REVERT: E  155 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6892 (mm-30)
REVERT: E  156 GLU cc_start: 0.7771 (tt0) cc_final: 0.7396 (tt0)
REVERT: E  163 ARG cc_start: 0.7215 (mmp80) cc_final: 0.6960 (mmp80)
REVERT: E  185 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7357 (pt0)
  outliers start: 28
  outliers final: 18
  residues processed: 164
  average time/residue: 0.6823
  time to fit residues: 120.3198
Evaluate side-chains
  166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LYS
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 125 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0060
   chunk 117 optimal weight:    3.9990
   chunk 147 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 122 optimal weight:    2.9990
   chunk 145 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 146 optimal weight:    0.8980
   chunk 148 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.5000

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.116102 restraints weight = 14362.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.13
r_work: 0.3322 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13065  Z= 0.154
  Angle     :  0.519   5.609  17780  Z= 0.273
  Chirality :  0.045   0.131   1955
  Planarity :  0.004   0.043   2265
  Dihedral  :  4.239  18.930   1715
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.09 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.23), residues: 1540
  helix:  1.57 (0.23), residues: 530
  sheet:  1.63 (0.28), residues: 435
  loop : -2.00 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 163 
 TYR   0.007   0.001   TYR E 148 
 PHE   0.011   0.001   PHE C 116 
 TRP   0.030   0.002   TRP C 206 
 HIS   0.004   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (13065)
  covalent geometry    : angle       0.51942 (17780)
  hydrogen bonds       : bond        0.03082 (  600)
  hydrogen bonds       : angle       4.31068 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 ASN cc_start: 0.7543 (m-40) cc_final: 0.7336 (m-40)
REVERT: A  124 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6452 (mp10)
REVERT: A  150 GLU cc_start: 0.7836 (pm20) cc_final: 0.7414 (mp0)
REVERT: A  155 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6833 (mm-30)
REVERT: A  156 GLU cc_start: 0.7700 (tt0) cc_final: 0.7266 (tt0)
REVERT: A  163 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6987 (mmp80)
REVERT: B   27 ASN cc_start: 0.8224 (t0) cc_final: 0.7855 (t0)
REVERT: B   36 ASP cc_start: 0.8985 (t0) cc_final: 0.8578 (t70)
REVERT: B   90 LYS cc_start: 0.8386 (pttt) cc_final: 0.7861 (ptpp)
REVERT: B   93 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8211 (mtp)
REVERT: B  137 ASN cc_start: 0.7788 (p0) cc_final: 0.7522 (p0)
REVERT: B  145 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7874 (tt)
REVERT: B  155 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6686 (mm-30)
REVERT: B  174 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7552 (ttm-80)
REVERT: C   36 ASP cc_start: 0.8908 (t0) cc_final: 0.8523 (t70)
REVERT: C   90 LYS cc_start: 0.8223 (pttt) cc_final: 0.7646 (ptpp)
REVERT: C  150 GLU cc_start: 0.7786 (pm20) cc_final: 0.7262 (mp0)
REVERT: C  155 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6700 (mm-30)
REVERT: D   27 ASN cc_start: 0.8029 (t0) cc_final: 0.7356 (t0)
REVERT: D   30 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7287 (mt-10)
REVERT: D   34 LYS cc_start: 0.8313 (mttm) cc_final: 0.8030 (mmtp)
REVERT: D   69 ASN cc_start: 0.7426 (m-40) cc_final: 0.7188 (m-40)
REVERT: D   86 ASP cc_start: 0.7683 (t70) cc_final: 0.7409 (t0)
REVERT: D   90 LYS cc_start: 0.8299 (pttt) cc_final: 0.7792 (ptpp)
REVERT: D  137 ASN cc_start: 0.7626 (p0) cc_final: 0.7233 (p0)
REVERT: D  155 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6876 (mm-30)
REVERT: D  174 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7649 (ttm-80)
REVERT: D  187 GLU cc_start: 0.7457 (tt0) cc_final: 0.7150 (mt-10)
REVERT: E   36 ASP cc_start: 0.8819 (t0) cc_final: 0.8468 (t70)
REVERT: E  150 GLU cc_start: 0.7791 (pm20) cc_final: 0.7337 (mp0)
REVERT: E  155 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6985 (mm-30)
REVERT: E  156 GLU cc_start: 0.7739 (tt0) cc_final: 0.7452 (tt0)
REVERT: E  163 ARG cc_start: 0.7247 (mmp80) cc_final: 0.6967 (mmp80)
REVERT: E  185 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7345 (pt0)
  outliers start: 30
  outliers final: 21
  residues processed: 165
  average time/residue: 0.7617
  time to fit residues: 134.6581
Evaluate side-chains
  170 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 140 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.151787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.119084 restraints weight = 14349.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.16
r_work: 0.3372 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13065  Z= 0.101
  Angle     :  0.473   5.942  17780  Z= 0.247
  Chirality :  0.044   0.133   1955
  Planarity :  0.004   0.044   2265
  Dihedral  :  3.964  18.102   1715
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.16 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.23), residues: 1540
  helix:  1.69 (0.23), residues: 530
  sheet:  1.74 (0.27), residues: 435
  loop : -1.99 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 163 
 TYR   0.007   0.001   TYR B 203 
 PHE   0.008   0.001   PHE B 116 
 TRP   0.034   0.001   TRP C 206 
 HIS   0.002   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (13065)
  covalent geometry    : angle       0.47266 (17780)
  hydrogen bonds       : bond        0.02625 (  600)
  hydrogen bonds       : angle       4.08979 ( 1995)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 GLU cc_start: 0.7819 (pm20) cc_final: 0.7401 (mp0)
REVERT: A  155 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6825 (mm-30)
REVERT: A  156 GLU cc_start: 0.7817 (tt0) cc_final: 0.7449 (tt0)
REVERT: A  163 ARG cc_start: 0.7278 (mmt90) cc_final: 0.7064 (mmp80)
REVERT: B   27 ASN cc_start: 0.8142 (t0) cc_final: 0.7847 (t0)
REVERT: B   69 ASN cc_start: 0.7401 (m-40) cc_final: 0.7149 (m-40)
REVERT: B   90 LYS cc_start: 0.8328 (pttt) cc_final: 0.7794 (ptpp)
REVERT: B   93 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8263 (mtp)
REVERT: B  137 ASN cc_start: 0.7629 (p0) cc_final: 0.7320 (p0)
REVERT: B  150 GLU cc_start: 0.7722 (pm20) cc_final: 0.7113 (mp0)
REVERT: B  155 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6629 (mm-30)
REVERT: B  156 GLU cc_start: 0.7789 (tt0) cc_final: 0.7388 (tt0)
REVERT: B  174 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7507 (ttm-80)
REVERT: C   90 LYS cc_start: 0.8182 (pttt) cc_final: 0.7654 (ptpp)
REVERT: C   93 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8319 (mtp)
REVERT: C  150 GLU cc_start: 0.7673 (pm20) cc_final: 0.7172 (mp0)
REVERT: C  155 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6752 (mm-30)
REVERT: D   27 ASN cc_start: 0.7866 (t0) cc_final: 0.7282 (t0)
REVERT: D   30 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7293 (mt-10)
REVERT: D   34 LYS cc_start: 0.8283 (mttm) cc_final: 0.8026 (mttp)
REVERT: D   69 ASN cc_start: 0.7400 (m-40) cc_final: 0.7149 (m-40)
REVERT: D   86 ASP cc_start: 0.7664 (t70) cc_final: 0.7387 (t0)
REVERT: D   90 LYS cc_start: 0.8261 (pttt) cc_final: 0.7728 (ptpp)
REVERT: D  137 ASN cc_start: 0.7483 (p0) cc_final: 0.7120 (p0)
REVERT: D  155 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6833 (mm-30)
REVERT: D  174 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7617 (ttm-80)
REVERT: D  187 GLU cc_start: 0.7473 (tt0) cc_final: 0.7179 (mt-10)
REVERT: E   34 LYS cc_start: 0.8348 (mttm) cc_final: 0.8141 (mmtp)
REVERT: E  155 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6849 (mm-30)
REVERT: E  163 ARG cc_start: 0.7196 (mmp80) cc_final: 0.6957 (mmp80)
REVERT: E  185 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7409 (pt0)
  outliers start: 29
  outliers final: 19
  residues processed: 166
  average time/residue: 0.7039
  time to fit residues: 125.7121
Evaluate side-chains
  168 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 109 optimal weight:    0.0670
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 5 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0060
   chunk 138 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    0.3980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.3534

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.155593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.123010 restraints weight = 14255.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.17
r_work: 0.3392 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13065  Z= 0.086
  Angle     :  0.452   5.656  17780  Z= 0.235
  Chirality :  0.043   0.135   1955
  Planarity :  0.004   0.044   2265
  Dihedral  :  3.708  17.542   1715
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.45 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.22), residues: 1540
  helix:  1.77 (0.23), residues: 530
  sheet:  1.78 (0.27), residues: 435
  loop : -1.96 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 163 
 TYR   0.006   0.001   TYR B 203 
 PHE   0.007   0.001   PHE D 106 
 TRP   0.036   0.001   TRP C 206 
 HIS   0.001   0.000   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 (13065)
  covalent geometry    : angle       0.45178 (17780)
  hydrogen bonds       : bond        0.02382 (  600)
  hydrogen bonds       : angle       3.86167 ( 1995)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4101.26 seconds
wall clock time: 70 minutes 30.54 seconds (4230.54 seconds total)