Starting phenix.real_space_refine
on Sun Aug 24 14:23:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8won_37693/08_2025/8won_37693.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8won_37693/08_2025/8won_37693.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8won_37693/08_2025/8won_37693.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8won_37693/08_2025/8won_37693.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8won_37693/08_2025/8won_37693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8won_37693/08_2025/8won_37693.map"
  }
  resolution = 2.69
  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=   0.001 sd=   0.168
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C   13280      2.51       5
     N    3510      2.21       5
     O    3910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20720
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2072
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 20, 'TRANS': 244}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 2.45, per 1000 atoms: 0.12
  Number of scatterers: 20720
  At special positions: 0
  Unit cell: (115.648, 123.968, 139.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    3910      8.00
     N    3510      7.00
     C   13280      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: 1.80
  Conformation dependent library (CDL) restraints added in 952.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4960

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 40 sheets defined
      27.5% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 120 through 147
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 3.543A  pdb=" N   ALA A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 170 through 181
    Processing helix  chain 'A' and resid 191 through 205
    Processing helix  chain 'A' and resid 297 through 299
      No H-bonds generated for 'chain 'A' and resid 297 through 299'
    Processing helix  chain 'B' and resid 45 through 50
    Processing helix  chain 'B' and resid 120 through 147
    Processing helix  chain 'B' and resid 151 through 156
      removed outlier: 3.543A  pdb=" N   ALA B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'B' and resid 170 through 181
    Processing helix  chain 'B' and resid 191 through 205
    Processing helix  chain 'B' and resid 297 through 299
      No H-bonds generated for 'chain 'B' and resid 297 through 299'
    Processing helix  chain 'C' and resid 45 through 50
    Processing helix  chain 'C' and resid 120 through 147
    Processing helix  chain 'C' and resid 151 through 156
      removed outlier: 3.544A  pdb=" N   ALA C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'C' and resid 170 through 181
    Processing helix  chain 'C' and resid 191 through 205
    Processing helix  chain 'C' and resid 297 through 299
      No H-bonds generated for 'chain 'C' and resid 297 through 299'
    Processing helix  chain 'D' and resid 45 through 50
    Processing helix  chain 'D' and resid 120 through 147
    Processing helix  chain 'D' and resid 151 through 156
      removed outlier: 3.542A  pdb=" N   ALA D 156 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 159
      No H-bonds generated for 'chain 'D' and resid 157 through 159'
    Processing helix  chain 'D' and resid 170 through 181
    Processing helix  chain 'D' and resid 191 through 205
    Processing helix  chain 'D' and resid 297 through 299
      No H-bonds generated for 'chain 'D' and resid 297 through 299'
    Processing helix  chain 'E' and resid 45 through 50
    Processing helix  chain 'E' and resid 120 through 147
    Processing helix  chain 'E' and resid 151 through 156
      removed outlier: 3.542A  pdb=" N   ALA E 156 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 159
      No H-bonds generated for 'chain 'E' and resid 157 through 159'
    Processing helix  chain 'E' and resid 170 through 181
    Processing helix  chain 'E' and resid 191 through 205
    Processing helix  chain 'E' and resid 297 through 299
      No H-bonds generated for 'chain 'E' and resid 297 through 299'
    Processing helix  chain 'F' and resid 45 through 50
    Processing helix  chain 'F' and resid 120 through 147
    Processing helix  chain 'F' and resid 151 through 156
      removed outlier: 3.543A  pdb=" N   ALA F 156 " --> pdb=" O   LEU F 152 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 157 through 159
      No H-bonds generated for 'chain 'F' and resid 157 through 159'
    Processing helix  chain 'F' and resid 170 through 181
    Processing helix  chain 'F' and resid 191 through 205
    Processing helix  chain 'F' and resid 297 through 299
      No H-bonds generated for 'chain 'F' and resid 297 through 299'
    Processing helix  chain 'G' and resid 45 through 50
    Processing helix  chain 'G' and resid 120 through 147
    Processing helix  chain 'G' and resid 151 through 156
      removed outlier: 3.543A  pdb=" N   ALA G 156 " --> pdb=" O   LEU G 152 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 157 through 159
      No H-bonds generated for 'chain 'G' and resid 157 through 159'
    Processing helix  chain 'G' and resid 170 through 181
    Processing helix  chain 'G' and resid 191 through 205
    Processing helix  chain 'G' and resid 297 through 299
      No H-bonds generated for 'chain 'G' and resid 297 through 299'
    Processing helix  chain 'H' and resid 45 through 50
    Processing helix  chain 'H' and resid 120 through 147
    Processing helix  chain 'H' and resid 151 through 156
      removed outlier: 3.543A  pdb=" N   ALA H 156 " --> pdb=" O   LEU H 152 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 157 through 159
      No H-bonds generated for 'chain 'H' and resid 157 through 159'
    Processing helix  chain 'H' and resid 170 through 181
    Processing helix  chain 'H' and resid 191 through 205
    Processing helix  chain 'H' and resid 297 through 299
      No H-bonds generated for 'chain 'H' and resid 297 through 299'
    Processing helix  chain 'I' and resid 45 through 50
    Processing helix  chain 'I' and resid 120 through 147
    Processing helix  chain 'I' and resid 151 through 156
      removed outlier: 3.542A  pdb=" N   ALA I 156 " --> pdb=" O   LEU I 152 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 157 through 159
      No H-bonds generated for 'chain 'I' and resid 157 through 159'
    Processing helix  chain 'I' and resid 170 through 181
    Processing helix  chain 'I' and resid 191 through 205
    Processing helix  chain 'I' and resid 297 through 299
      No H-bonds generated for 'chain 'I' and resid 297 through 299'
    Processing helix  chain 'J' and resid 45 through 50
    Processing helix  chain 'J' and resid 120 through 147
    Processing helix  chain 'J' and resid 151 through 156
      removed outlier: 3.542A  pdb=" N   ALA J 156 " --> pdb=" O   LEU J 152 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 157 through 159
      No H-bonds generated for 'chain 'J' and resid 157 through 159'
    Processing helix  chain 'J' and resid 170 through 181
    Processing helix  chain 'J' and resid 191 through 205
    Processing helix  chain 'J' and resid 297 through 299
      No H-bonds generated for 'chain 'J' and resid 297 through 299'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER A  51 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER A  51 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER A 284 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 65
      removed outlier: 3.530A  pdb=" N   ARG A  64 " --> pdb=" O   HIS A  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE A 162 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL A 307 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY A 306 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   THR A 240 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE A 220 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN A 218 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER B  51 " --> pdb=" O   VAL B 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER B  51 " --> pdb=" O   VAL B 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER B 284 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG B  64 " --> pdb=" O   HIS B  95 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE B 162 " --> pdb=" O   ASP B 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL B 307 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY B 306 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   THR B 240 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ILE B 220 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN B 218 " --> pdb=" O   PRO B 229 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER C  51 " --> pdb=" O   VAL C 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER C  51 " --> pdb=" O   VAL C 254 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   SER C 284 " --> pdb=" O   THR C 275 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG C  64 " --> pdb=" O   HIS C  95 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE C 162 " --> pdb=" O   ASP C 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL C 307 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY C 306 " --> pdb=" O   THR C 240 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   THR C 240 " --> pdb=" O   GLY C 306 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE C 220 " --> pdb=" O   ILE C 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN C 218 " --> pdb=" O   PRO C 229 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 51 through 54
      removed outlier: 4.451A  pdb=" N   SER D  51 " --> pdb=" O   VAL D 254 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 51 through 54
      removed outlier: 4.451A  pdb=" N   SER D  51 " --> pdb=" O   VAL D 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER D 284 " --> pdb=" O   THR D 275 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 65
      removed outlier: 3.530A  pdb=" N   ARG D  64 " --> pdb=" O   HIS D  95 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE D 162 " --> pdb=" O   ASP D 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL D 307 " --> pdb=" O   ILE D 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY D 306 " --> pdb=" O   THR D 240 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   THR D 240 " --> pdb=" O   GLY D 306 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE D 220 " --> pdb=" O   ILE D 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN D 218 " --> pdb=" O   PRO D 229 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER E  51 " --> pdb=" O   VAL E 254 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER E  51 " --> pdb=" O   VAL E 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER E 284 " --> pdb=" O   THR E 275 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG E  64 " --> pdb=" O   HIS E  95 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 163
      removed outlier: 6.760A  pdb=" N   ILE E 162 " --> pdb=" O   ASP E 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL E 307 " --> pdb=" O   ILE E 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY E 306 " --> pdb=" O   THR E 240 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   THR E 240 " --> pdb=" O   GLY E 306 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ILE E 220 " --> pdb=" O   ILE E 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN E 218 " --> pdb=" O   PRO E 229 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER F  51 " --> pdb=" O   VAL F 254 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER F  51 " --> pdb=" O   VAL F 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER F 284 " --> pdb=" O   THR F 275 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG F  64 " --> pdb=" O   HIS F  95 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE F 162 " --> pdb=" O   ASP F 305 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   VAL F 307 " --> pdb=" O   ILE F 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY F 306 " --> pdb=" O   THR F 240 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   THR F 240 " --> pdb=" O   GLY F 306 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ILE F 220 " --> pdb=" O   ILE F 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN F 218 " --> pdb=" O   PRO F 229 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'G' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER G  51 " --> pdb=" O   VAL G 254 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER G  51 " --> pdb=" O   VAL G 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER G 284 " --> pdb=" O   THR G 275 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG G  64 " --> pdb=" O   HIS G  95 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'G' and resid 161 through 163
      removed outlier: 6.762A  pdb=" N   ILE G 162 " --> pdb=" O   ASP G 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL G 307 " --> pdb=" O   ILE G 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY G 306 " --> pdb=" O   THR G 240 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   THR G 240 " --> pdb=" O   GLY G 306 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ILE G 220 " --> pdb=" O   ILE G 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN G 218 " --> pdb=" O   PRO G 229 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'H' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER H  51 " --> pdb=" O   VAL H 254 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'H' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER H  51 " --> pdb=" O   VAL H 254 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   SER H 284 " --> pdb=" O   THR H 275 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG H  64 " --> pdb=" O   HIS H  95 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'H' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE H 162 " --> pdb=" O   ASP H 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL H 307 " --> pdb=" O   ILE H 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY H 306 " --> pdb=" O   THR H 240 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   THR H 240 " --> pdb=" O   GLY H 306 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE H 220 " --> pdb=" O   ILE H 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN H 218 " --> pdb=" O   PRO H 229 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'I' and resid 51 through 54
      removed outlier: 4.451A  pdb=" N   SER I  51 " --> pdb=" O   VAL I 254 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'I' and resid 51 through 54
      removed outlier: 4.451A  pdb=" N   SER I  51 " --> pdb=" O   VAL I 254 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   SER I 284 " --> pdb=" O   THR I 275 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'I' and resid 59 through 65
      removed outlier: 3.530A  pdb=" N   ARG I  64 " --> pdb=" O   HIS I  95 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'I' and resid 161 through 163
      removed outlier: 6.761A  pdb=" N   ILE I 162 " --> pdb=" O   ASP I 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL I 307 " --> pdb=" O   ILE I 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY I 306 " --> pdb=" O   THR I 240 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   THR I 240 " --> pdb=" O   GLY I 306 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ILE I 220 " --> pdb=" O   ILE I 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN I 218 " --> pdb=" O   PRO I 229 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'J' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER J  51 " --> pdb=" O   VAL J 254 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'J' and resid 51 through 54
      removed outlier: 4.452A  pdb=" N   SER J  51 " --> pdb=" O   VAL J 254 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   SER J 284 " --> pdb=" O   THR J 275 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'J' and resid 59 through 65
      removed outlier: 3.529A  pdb=" N   ARG J  64 " --> pdb=" O   HIS J  95 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'J' and resid 161 through 163
      removed outlier: 6.760A  pdb=" N   ILE J 162 " --> pdb=" O   ASP J 305 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL J 307 " --> pdb=" O   ILE J 162 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY J 306 " --> pdb=" O   THR J 240 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   THR J 240 " --> pdb=" O   GLY J 306 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ILE J 220 " --> pdb=" O   ILE J 227 " (cutoff:3.500A)
      removed outlier: 10.306A  pdb=" N   GLN J 218 " --> pdb=" O   PRO J 229 " (cutoff:3.500A)

    980 hydrogen bonds defined for protein.
    2790 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: 4.56

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 3400
        1.29 -     1.42: 5299
        1.42 -     1.55: 12461
        1.55 -     1.67: 30
        1.67 -     1.80: 30
  Bond restraints: 21220
  Sorted by residual:
  bond pdb=" CA  ASN H  67 "
       pdb=" C   ASN H  67 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.08e-02 8.57e+03 5.62e+01
  bond pdb=" CA  ASN C  67 "
       pdb=" C   ASN C  67 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.08e-02 8.57e+03 5.61e+01
  bond pdb=" CA  ASN D  67 "
       pdb=" C   ASN D  67 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.08e-02 8.57e+03 5.61e+01
  bond pdb=" CA  ASN A  67 "
       pdb=" C   ASN A  67 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.08e-02 8.57e+03 5.59e+01
  bond pdb=" CA  ASN I  67 "
       pdb=" C   ASN I  67 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.08e-02 8.57e+03 5.59e+01
  ... (remaining 21215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 28295
        2.13 -     4.26: 645
        4.26 -     6.38: 89
        6.38 -     8.51: 41
        8.51 -    10.64: 10
  Bond angle restraints: 29080
  Sorted by residual:
  angle pdb=" N   VAL B  66 "
        pdb=" CA  VAL B  66 "
        pdb=" C   VAL B  66 "
      ideal   model   delta    sigma   weight residual
     110.72  119.03   -8.31 1.01e+00 9.80e-01 6.77e+01
  angle pdb=" N   VAL G  66 "
        pdb=" CA  VAL G  66 "
        pdb=" C   VAL G  66 "
      ideal   model   delta    sigma   weight residual
     110.72  119.02   -8.30 1.01e+00 9.80e-01 6.76e+01
  angle pdb=" N   VAL J  66 "
        pdb=" CA  VAL J  66 "
        pdb=" C   VAL J  66 "
      ideal   model   delta    sigma   weight residual
     110.72  119.00   -8.28 1.01e+00 9.80e-01 6.73e+01
  angle pdb=" N   VAL A  66 "
        pdb=" CA  VAL A  66 "
        pdb=" C   VAL A  66 "
      ideal   model   delta    sigma   weight residual
     110.72  119.00   -8.28 1.01e+00 9.80e-01 6.72e+01
  angle pdb=" N   VAL C  66 "
        pdb=" CA  VAL C  66 "
        pdb=" C   VAL C  66 "
      ideal   model   delta    sigma   weight residual
     110.72  118.99   -8.27 1.01e+00 9.80e-01 6.71e+01
  ... (remaining 29075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 10940
       17.27 -    34.53: 1340
       34.53 -    51.80: 270
       51.80 -    69.06: 80
       69.06 -    86.33: 20
  Dihedral angle restraints: 12650
    sinusoidal: 4950
      harmonic: 7700
  Sorted by residual:
  dihedral pdb=" CA  VAL D 145 "
           pdb=" C   VAL D 145 "
           pdb=" N   ASN D 146 "
           pdb=" CA  ASN D 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.75  -21.25     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  VAL I 145 "
           pdb=" C   VAL I 145 "
           pdb=" N   ASN I 146 "
           pdb=" CA  ASN I 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.75  -21.25     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  VAL H 145 "
           pdb=" C   VAL H 145 "
           pdb=" N   ASN H 146 "
           pdb=" CA  ASN H 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.76  -21.24     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 12647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 2783
       0.065 -    0.129: 578
       0.129 -    0.194: 49
       0.194 -    0.258: 20
       0.258 -    0.323: 20
  Chirality restraints: 3450
  Sorted by residual:
  chirality pdb=" CA  PRO H  68 "
            pdb=" N   PRO H  68 "
            pdb=" C   PRO H  68 "
            pdb=" CB  PRO H  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  PRO C  68 "
            pdb=" N   PRO C  68 "
            pdb=" C   PRO C  68 "
            pdb=" CB  PRO C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  PRO G  68 "
            pdb=" N   PRO G  68 "
            pdb=" C   PRO G  68 "
            pdb=" CB  PRO G  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.58e+00
  ... (remaining 3447 not shown)

  Planarity restraints: 3740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN I  67 "    0.052 5.00e-02 4.00e+02   7.77e-02 9.67e+00
        pdb=" N   PRO I  68 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO I  68 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO I  68 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  67 "    0.052 5.00e-02 4.00e+02   7.76e-02 9.63e+00
        pdb=" N   PRO G  68 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO G  68 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G  68 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  67 "    0.052 5.00e-02 4.00e+02   7.76e-02 9.63e+00
        pdb=" N   PRO C  68 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C  68 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C  68 "    0.046 5.00e-02 4.00e+02
  ... (remaining 3737 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2347
        2.75 -     3.29: 18481
        3.29 -     3.82: 34433
        3.82 -     4.36: 43035
        4.36 -     4.90: 72542
  Nonbonded interactions: 170838
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU J 143 "
            pdb=" ND2 ASN J 147 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OE1 GLU I 143 "
            pdb=" ND2 ASN I 147 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OE1 GLU D 143 "
            pdb=" ND2 ASN D 147 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OE1 GLU E 143 "
            pdb=" ND2 ASN E 147 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE1 GLU A 143 "
            pdb=" ND2 ASN A 147 "
     model   vdw
     2.213 3.120
  ... (remaining 170833 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             2.210
  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:             0.030
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     18.610
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081  21220  Z= 0.444
  Angle     :  0.787  10.638  29080  Z= 0.439
  Chirality :  0.059   0.323   3450
  Planarity :  0.008   0.078   3740
  Dihedral  : 16.527  86.329   7690
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 16.20 %
    Favored  : 83.36 %
  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: -0.08 (0.16), residues: 2610
  helix:  0.53 (0.19), residues: 670
  sheet:  1.44 (0.19), residues: 730
  loop : -1.39 (0.17), residues: 1210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  64 
 TYR   0.012   0.003   TYR I 315 
 PHE   0.015   0.002   PHE E 188 
 TRP   0.009   0.002   TRP I  52 
 HIS   0.003   0.001   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 (21220)
  covalent geometry    : angle       0.78718 (29080)
  hydrogen bonds       : bond        0.17514 (  910)
  hydrogen bonds       : angle       6.37392 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 378
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 GLU cc_start: 0.7913 (tt0) cc_final: 0.7671 (pm20)
REVERT: E  271 SER cc_start: 0.8482 (t) cc_final: 0.8261 (t)
REVERT: H  271 SER cc_start: 0.8486 (t) cc_final: 0.8265 (t)
REVERT: I  139 ARG cc_start: 0.8205 (tpt-90) cc_final: 0.7975 (tmt-80)
REVERT: I  249 GLU cc_start: 0.7894 (tt0) cc_final: 0.7667 (pm20)
  outliers start: 10
  outliers final: 4
  residues processed: 382
  average time/residue: 0.8201
  time to fit residues: 345.6418
Evaluate side-chains
  254 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 250
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain E residue  100 THR
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain I residue  100 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 197 optimal weight:    9.9990
   chunk 215 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 132 optimal weight:    8.9990
   chunk 248 optimal weight:    7.9990
   chunk 207 optimal weight:    2.9990
   chunk 155 optimal weight:    6.9990
   chunk 244 optimal weight:    0.7980
   chunk 183 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 258 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
B 122 HIS
C 128 GLN
C 191 HIS
C 218 GLN
D 252 GLN
D 316 GLN
E 313 HIS
F 128 GLN
F 191 HIS
F 218 GLN
G 252 GLN
G 316 GLN
H 313 HIS
I  63 ASN
J 122 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.174699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.147003 restraints weight = 22965.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 1.59
r_work: 0.3535 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  21220  Z= 0.133
  Angle     :  0.558   6.735  29080  Z= 0.295
  Chirality :  0.047   0.154   3450
  Planarity :  0.006   0.045   3740
  Dihedral  :  4.975  20.766   2894
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.61 %
    Favored  : 78.47 %
  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:  0.40 (0.16), residues: 2610
  helix:  1.24 (0.19), residues: 670
  sheet:  1.62 (0.19), residues: 710
  loop : -1.17 (0.17), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.011   0.001   TYR B 290 
 PHE   0.012   0.001   PHE I 188 
 TRP   0.010   0.002   TRP D  52 
 HIS   0.005   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (21220)
  covalent geometry    : angle       0.55766 (29080)
  hydrogen bonds       : bond        0.04969 (  910)
  hydrogen bonds       : angle       4.90001 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 308
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8467 (ttp-170)
REVERT: A  139 ARG cc_start: 0.8789 (tpt170) cc_final: 0.8001 (ttp-110)
REVERT: A  236 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7611 (pm20)
REVERT: C  134 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7335 (mp0)
REVERT: C  310 ASP cc_start: 0.6950 (p0) cc_final: 0.6386 (t0)
REVERT: D   97 ARG cc_start: 0.6958 (tpt170) cc_final: 0.6734 (tpt170)
REVERT: D  107 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7108 (tm)
REVERT: D  250 GLU cc_start: 0.7829 (tp30) cc_final: 0.7407 (mp0)
REVERT: D  251 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7360 (ptm160)
REVERT: E   33 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7935 (ttmt)
REVERT: F   97 ARG cc_start: 0.6787 (tpt-90) cc_final: 0.6059 (ptm160)
REVERT: F  134 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7329 (mp0)
REVERT: F  180 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7691 (mttp)
REVERT: F  310 ASP cc_start: 0.6962 (p0) cc_final: 0.6395 (t0)
REVERT: G   97 ARG cc_start: 0.6948 (tpt170) cc_final: 0.6726 (tpt170)
REVERT: G  250 GLU cc_start: 0.7882 (tp30) cc_final: 0.7416 (mp0)
REVERT: G  251 ARG cc_start: 0.7706 (ptp-110) cc_final: 0.7370 (ptm160)
REVERT: H   33 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7963 (ttmt)
REVERT: I  139 ARG cc_start: 0.8807 (tpt-90) cc_final: 0.7986 (ttp-110)
REVERT: I  236 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7626 (pm20)
  outliers start: 44
  outliers final: 10
  residues processed: 329
  average time/residue: 0.7285
  time to fit residues: 267.3950
Evaluate side-chains
  284 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 268
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue  105 SER
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain F residue  180 LYS
Chi-restraints excluded: chain F residue  240 THR
Chi-restraints excluded: chain G residue  132 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue  105 SER
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain I residue  177 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 210 optimal weight:    3.9990
   chunk 195 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 259 optimal weight:    5.9990
   chunk 106 optimal weight:    0.8980
   chunk 155 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
C  63 ASN
C 160 GLN
D 252 GLN
F  63 ASN
F 160 GLN
G 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.170221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.142473 restraints weight = 23032.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.60
r_work: 0.3465 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3361 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  21220  Z= 0.201
  Angle     :  0.634   6.600  29080  Z= 0.332
  Chirality :  0.051   0.160   3450
  Planarity :  0.007   0.049   3740
  Dihedral  :  5.197  21.006   2890
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.52 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.16), residues: 2610
  helix:  0.96 (0.19), residues: 670
  sheet:  1.33 (0.19), residues: 710
  loop : -1.29 (0.17), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  61 
 TYR   0.014   0.002   TYR D 315 
 PHE   0.019   0.002   PHE F 188 
 TRP   0.011   0.002   TRP D 182 
 HIS   0.006   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (21220)
  covalent geometry    : angle       0.63365 (29080)
  hydrogen bonds       : bond        0.06206 (  910)
  hydrogen bonds       : angle       5.18115 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 271
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  114 VAL cc_start: 0.3595 (OUTLIER) cc_final: 0.3386 (t)
REVERT: A  139 ARG cc_start: 0.8804 (tpt170) cc_final: 0.8046 (ttp-110)
REVERT: A  236 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7569 (pm20)
REVERT: A  249 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7673 (pm20)
REVERT: B   33 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6423 (mttm)
REVERT: C   97 ARG cc_start: 0.7038 (tpt-90) cc_final: 0.6279 (ptm160)
REVERT: C  134 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7033 (mp0)
REVERT: C  273 ARG cc_start: 0.6893 (ttp-110) cc_final: 0.6043 (ttp-170)
REVERT: D   61 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6648 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7064 (tm)
REVERT: D  110 VAL cc_start: 0.6114 (OUTLIER) cc_final: 0.5900 (t)
REVERT: D  251 ARG cc_start: 0.7636 (ptp-110) cc_final: 0.7426 (ptm160)
REVERT: E   33 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7991 (ttmt)
REVERT: E  139 ARG cc_start: 0.8111 (tpt-90) cc_final: 0.7646 (ttp80)
REVERT: F   61 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7342 (ttm-80)
REVERT: F   97 ARG cc_start: 0.7006 (tpt-90) cc_final: 0.6271 (ptm160)
REVERT: F  134 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7048 (mp0)
REVERT: F  273 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6048 (ttp-170)
REVERT: G   61 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6641 (tmm-80)
REVERT: G  110 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.5874 (t)
REVERT: G  251 ARG cc_start: 0.7642 (ptp-110) cc_final: 0.7421 (ptm160)
REVERT: H   33 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7866 (ttmt)
REVERT: H  139 ARG cc_start: 0.8090 (tpt-90) cc_final: 0.7650 (ttp80)
REVERT: I   61 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8552 (ttp-170)
REVERT: I  114 VAL cc_start: 0.3642 (OUTLIER) cc_final: 0.3442 (t)
REVERT: I  139 ARG cc_start: 0.8836 (tpt-90) cc_final: 0.8043 (ttp-110)
REVERT: I  236 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7565 (pm20)
REVERT: I  249 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7692 (pm20)
REVERT: J   33 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6439 (mttm)
  outliers start: 89
  outliers final: 35
  residues processed: 327
  average time/residue: 0.7461
  time to fit residues: 272.1858
Evaluate side-chains
  290 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 242
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain B residue   33 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue  105 SER
Chi-restraints excluded: chain E residue  162 ILE
Chi-restraints excluded: chain E residue  273 ARG
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain F residue  180 LYS
Chi-restraints excluded: chain F residue  240 THR
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  132 THR
Chi-restraints excluded: chain G residue  136 ILE
Chi-restraints excluded: chain G residue  214 MET
Chi-restraints excluded: chain G residue  271 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue  105 SER
Chi-restraints excluded: chain H residue  162 ILE
Chi-restraints excluded: chain H residue  273 ARG
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  114 VAL
Chi-restraints excluded: chain I residue  177 LEU
Chi-restraints excluded: chain I residue  249 GLU
Chi-restraints excluded: chain I residue  263 VAL
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  177 LEU
Chi-restraints excluded: chain J residue  284 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 186 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 235 optimal weight:    0.2980
   chunk 204 optimal weight:    3.9990
   chunk 172 optimal weight:    2.9990
   chunk 203 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 150 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS
D 122 HIS
F 122 HIS
G 122 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.170432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.142492 restraints weight = 23244.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 1.63
r_work: 0.3484 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  21220  Z= 0.159
  Angle     :  0.580   7.052  29080  Z= 0.304
  Chirality :  0.048   0.155   3450
  Planarity :  0.006   0.050   3740
  Dihedral  :  5.015  20.189   2890
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.43 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.16), residues: 2610
  helix:  1.11 (0.19), residues: 670
  sheet:  1.16 (0.19), residues: 710
  loop : -1.28 (0.17), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 251 
 TYR   0.012   0.002   TYR C 150 
 PHE   0.018   0.002   PHE C 188 
 TRP   0.010   0.002   TRP I  52 
 HIS   0.005   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (21220)
  covalent geometry    : angle       0.58000 (29080)
  hydrogen bonds       : bond        0.05345 (  910)
  hydrogen bonds       : angle       4.97347 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 276
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  139 ARG cc_start: 0.8786 (tpt170) cc_final: 0.7968 (ttp-110)
REVERT: A  236 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7498 (pm20)
REVERT: A  249 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7602 (pm20)
REVERT: B   33 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6511 (mttm)
REVERT: C   97 ARG cc_start: 0.6982 (tpt-90) cc_final: 0.6080 (ptm160)
REVERT: C  134 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7186 (mp0)
REVERT: C  273 ARG cc_start: 0.6916 (ttp-110) cc_final: 0.6054 (ttp-170)
REVERT: C  277 ILE cc_start: 0.1895 (OUTLIER) cc_final: 0.1647 (mm)
REVERT: D   61 ARG cc_start: 0.7251 (ttm110) cc_final: 0.6655 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.6907 (tm)
REVERT: D  110 VAL cc_start: 0.6140 (OUTLIER) cc_final: 0.5939 (t)
REVERT: D  132 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7569 (p)
REVERT: D  239 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7109 (m)
REVERT: D  251 ARG cc_start: 0.7619 (ptp-110) cc_final: 0.7387 (ptm160)
REVERT: E   33 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7908 (ttmt)
REVERT: E   59 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7917 (mt)
REVERT: E  139 ARG cc_start: 0.7977 (tpt-90) cc_final: 0.7492 (ttp80)
REVERT: F   61 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7304 (ttm-80)
REVERT: F   97 ARG cc_start: 0.6953 (tpt-90) cc_final: 0.6186 (ptm160)
REVERT: F  134 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7174 (mp0)
REVERT: F  273 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.6068 (ttp-170)
REVERT: F  277 ILE cc_start: 0.1883 (OUTLIER) cc_final: 0.1643 (mm)
REVERT: G   61 ARG cc_start: 0.7261 (ttm110) cc_final: 0.6674 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.6885 (tm)
REVERT: G  110 VAL cc_start: 0.6134 (OUTLIER) cc_final: 0.5930 (t)
REVERT: G  132 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7593 (p)
REVERT: G  239 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7100 (m)
REVERT: G  251 ARG cc_start: 0.7628 (ptp-110) cc_final: 0.7381 (ptm160)
REVERT: H   33 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7879 (ttmt)
REVERT: H   59 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7914 (mt)
REVERT: H  139 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7497 (ttp80)
REVERT: I   61 ARG cc_start: 0.8736 (ttm170) cc_final: 0.8534 (ttp-170)
REVERT: I  139 ARG cc_start: 0.8806 (tpt-90) cc_final: 0.7974 (ttp-110)
REVERT: I  236 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7473 (pm20)
REVERT: I  249 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7599 (pm20)
  outliers start: 94
  outliers final: 34
  residues processed: 337
  average time/residue: 0.7385
  time to fit residues: 277.9607
Evaluate side-chains
  298 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 245
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue   33 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   59 ILE
Chi-restraints excluded: chain E residue  105 SER
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  159 GLU
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain F residue  180 LYS
Chi-restraints excluded: chain F residue  240 THR
Chi-restraints excluded: chain F residue  277 ILE
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  132 THR
Chi-restraints excluded: chain G residue  239 THR
Chi-restraints excluded: chain G residue  271 SER
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue   59 ILE
Chi-restraints excluded: chain H residue  105 SER
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  159 GLU
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  177 LEU
Chi-restraints excluded: chain I residue  249 GLU
Chi-restraints excluded: chain I residue  263 VAL
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  177 LEU
Chi-restraints excluded: chain J residue  284 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 239 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 259 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 224 optimal weight:    2.9990
   chunk 226 optimal weight:    4.9990
   chunk 187 optimal weight:   10.0000
   chunk 204 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
C 128 GLN
F 128 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.170964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.143360 restraints weight = 23158.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.60
r_work: 0.3492 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  21220  Z= 0.144
  Angle     :  0.562   6.979  29080  Z= 0.294
  Chirality :  0.048   0.175   3450
  Planarity :  0.006   0.050   3740
  Dihedral  :  4.857  19.834   2890
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.26 %
    Favored  : 77.07 %
  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:  0.10 (0.16), residues: 2610
  helix:  1.25 (0.19), residues: 670
  sheet:  0.95 (0.18), residues: 730
  loop : -1.21 (0.18), residues: 1210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J 251 
 TYR   0.013   0.001   TYR E 215 
 PHE   0.017   0.002   PHE F 188 
 TRP   0.010   0.002   TRP D 182 
 HIS   0.005   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (21220)
  covalent geometry    : angle       0.56179 (29080)
  hydrogen bonds       : bond        0.05042 (  910)
  hydrogen bonds       : angle       4.89189 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 251
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7509 (pm20)
REVERT: A  249 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7599 (pm20)
REVERT: B   33 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6658 (mttp)
REVERT: C   61 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7263 (ttm-80)
REVERT: C   97 ARG cc_start: 0.6966 (tpt-90) cc_final: 0.6137 (ptm160)
REVERT: C  134 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7172 (mp0)
REVERT: C  310 ASP cc_start: 0.6911 (p0) cc_final: 0.6342 (t0)
REVERT: D   61 ARG cc_start: 0.7294 (ttm110) cc_final: 0.6712 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6862 (tm)
REVERT: D  132 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7560 (p)
REVERT: D  239 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7196 (m)
REVERT: D  250 GLU cc_start: 0.7814 (tp30) cc_final: 0.7350 (mp0)
REVERT: D  251 ARG cc_start: 0.7613 (ptp-110) cc_final: 0.7392 (ptm160)
REVERT: E   33 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7868 (ttmt)
REVERT: E   59 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7995 (mt)
REVERT: E   61 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7275 (tpp80)
REVERT: E  139 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7483 (ttp80)
REVERT: F   61 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7299 (ttm-80)
REVERT: F   97 ARG cc_start: 0.6960 (tpt-90) cc_final: 0.6183 (ptm160)
REVERT: F  134 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7185 (mp0)
REVERT: F  310 ASP cc_start: 0.6903 (p0) cc_final: 0.6350 (t0)
REVERT: G   61 ARG cc_start: 0.7321 (ttm110) cc_final: 0.6738 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6854 (tm)
REVERT: G  132 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7597 (p)
REVERT: G  239 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7195 (m)
REVERT: G  250 GLU cc_start: 0.7836 (tp30) cc_final: 0.7339 (mp0)
REVERT: G  251 ARG cc_start: 0.7606 (ptp-110) cc_final: 0.7384 (ptm160)
REVERT: H   33 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7842 (ttmt)
REVERT: H   59 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7985 (mt)
REVERT: H   61 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7304 (tpp80)
REVERT: H  139 ARG cc_start: 0.7972 (tpt-90) cc_final: 0.7476 (ttp80)
REVERT: I   61 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8462 (ttp-170)
REVERT: I  139 ARG cc_start: 0.8804 (tpt-90) cc_final: 0.7969 (ttp-110)
REVERT: I  236 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7486 (pm20)
REVERT: I  249 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7598 (pm20)
REVERT: J   33 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6320 (mttm)
  outliers start: 84
  outliers final: 38
  residues processed: 307
  average time/residue: 0.7285
  time to fit residues: 250.4088
Evaluate side-chains
  302 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 246
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue   33 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   59 ILE
Chi-restraints excluded: chain E residue  105 SER
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  159 GLU
Chi-restraints excluded: chain E residue  273 ARG
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue   61 ARG
Chi-restraints excluded: chain F residue  110 VAL
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain F residue  180 LYS
Chi-restraints excluded: chain F residue  240 THR
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  132 THR
Chi-restraints excluded: chain G residue  214 MET
Chi-restraints excluded: chain G residue  239 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue   59 ILE
Chi-restraints excluded: chain H residue  105 SER
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  159 GLU
Chi-restraints excluded: chain H residue  273 ARG
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  177 LEU
Chi-restraints excluded: chain I residue  249 GLU
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  177 LEU
Chi-restraints excluded: chain J residue  277 ILE
Chi-restraints excluded: chain J residue  284 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 114 optimal weight:    5.9990
   chunk 259 optimal weight:    7.9990
   chunk 208 optimal weight:    5.9990
   chunk 204 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 142 optimal weight:    2.9990
   chunk 236 optimal weight:    3.9990
   chunk 176 optimal weight:    3.9990
   chunk 173 optimal weight:    0.2980
   overall best weight:    1.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.172837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.145140 restraints weight = 23062.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 1.54
r_work: 0.3504 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  21220  Z= 0.154
  Angle     :  0.579   6.524  29080  Z= 0.302
  Chirality :  0.048   0.180   3450
  Planarity :  0.006   0.050   3740
  Dihedral  :  4.876  19.945   2890
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.83 %
    Favored  : 76.72 %
  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:  0.08 (0.16), residues: 2610
  helix:  1.23 (0.19), residues: 670
  sheet:  0.92 (0.18), residues: 730
  loop : -1.20 (0.18), residues: 1210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 251 
 TYR   0.013   0.002   TYR E 215 
 PHE   0.018   0.002   PHE F 188 
 TRP   0.011   0.002   TRP D 182 
 HIS   0.005   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (21220)
  covalent geometry    : angle       0.57889 (29080)
  hydrogen bonds       : bond        0.05244 (  910)
  hydrogen bonds       : angle       4.93699 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 260
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7695 (pm20)
REVERT: A  249 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7674 (pm20)
REVERT: B   33 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6554 (mttm)
REVERT: B  316 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6437 (tm-30)
REVERT: C   61 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7363 (ttm-80)
REVERT: C   97 ARG cc_start: 0.7087 (tpt-90) cc_final: 0.6319 (ptm160)
REVERT: C  134 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7203 (mp0)
REVERT: C  273 ARG cc_start: 0.6886 (ttp-110) cc_final: 0.6072 (ttp-110)
REVERT: C  310 ASP cc_start: 0.6952 (p0) cc_final: 0.6514 (t0)
REVERT: D   61 ARG cc_start: 0.7331 (ttm110) cc_final: 0.6760 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.6999 (tm)
REVERT: D  130 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7850 (tmm160)
REVERT: D  132 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7764 (p)
REVERT: D  239 THR cc_start: 0.7823 (OUTLIER) cc_final: 0.7223 (m)
REVERT: D  250 GLU cc_start: 0.7862 (tp30) cc_final: 0.7419 (mp0)
REVERT: E   33 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7936 (ttmt)
REVERT: E   59 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8241 (mt)
REVERT: E   61 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7327 (tpp80)
REVERT: E  139 ARG cc_start: 0.8098 (tpt-90) cc_final: 0.7663 (ttp80)
REVERT: F   61 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7365 (ttm-80)
REVERT: F   97 ARG cc_start: 0.7096 (tpt-90) cc_final: 0.6349 (ptm160)
REVERT: F  134 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7250 (mp0)
REVERT: F  273 ARG cc_start: 0.6891 (ttp-110) cc_final: 0.6098 (ttp-110)
REVERT: F  310 ASP cc_start: 0.6938 (p0) cc_final: 0.6531 (t0)
REVERT: G   61 ARG cc_start: 0.7350 (ttm110) cc_final: 0.6777 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7025 (tm)
REVERT: G  239 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7223 (m)
REVERT: G  250 GLU cc_start: 0.7853 (tp30) cc_final: 0.7405 (mp0)
REVERT: H   33 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7865 (ttmt)
REVERT: H   59 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8230 (mt)
REVERT: H   61 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7304 (tpp80)
REVERT: H  139 ARG cc_start: 0.8100 (tpt-90) cc_final: 0.7662 (ttp80)
REVERT: I   61 ARG cc_start: 0.8724 (ttm170) cc_final: 0.8453 (ttp-170)
REVERT: I  139 ARG cc_start: 0.8843 (tpt-90) cc_final: 0.8072 (ttp-110)
REVERT: I  236 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7667 (pm20)
REVERT: I  249 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7659 (pm20)
REVERT: J   33 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6771 (mttp)
REVERT: J  316 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6409 (tm-30)
  outliers start: 79
  outliers final: 42
  residues processed: 311
  average time/residue: 0.6971
  time to fit residues: 242.4860
Evaluate side-chains
  302 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 241
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue   33 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain C residue   61 ARG
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain D residue  239 THR
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   59 ILE
Chi-restraints excluded: chain E residue  105 SER
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  159 GLU
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue   61 ARG
Chi-restraints excluded: chain F residue  110 VAL
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain F residue  180 LYS
Chi-restraints excluded: chain F residue  240 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  117 LEU
Chi-restraints excluded: chain G residue  214 MET
Chi-restraints excluded: chain G residue  239 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue   59 ILE
Chi-restraints excluded: chain H residue  105 SER
Chi-restraints excluded: chain H residue  159 GLU
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  177 LEU
Chi-restraints excluded: chain I residue  249 GLU
Chi-restraints excluded: chain I residue  263 VAL
Chi-restraints excluded: chain I residue  271 SER
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  177 LEU
Chi-restraints excluded: chain J residue  277 ILE
Chi-restraints excluded: chain J residue  284 SER
Chi-restraints excluded: chain J residue  316 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 191 optimal weight:    0.7980
   chunk 78 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 179 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 251 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 234 optimal weight:    6.9990
   overall best weight:    1.7586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.172932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.145193 restraints weight = 23139.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.53
r_work: 0.3502 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  21220  Z= 0.153
  Angle     :  0.579   6.499  29080  Z= 0.302
  Chirality :  0.048   0.189   3450
  Planarity :  0.006   0.050   3740
  Dihedral  :  4.850  19.889   2890
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.13 %
    Favored  : 76.81 %
  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:  0.12 (0.16), residues: 2610
  helix:  1.28 (0.19), residues: 670
  sheet:  0.91 (0.18), residues: 730
  loop : -1.17 (0.18), residues: 1210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J 251 
 TYR   0.015   0.002   TYR E 215 
 PHE   0.018   0.002   PHE C 188 
 TRP   0.010   0.002   TRP D 182 
 HIS   0.005   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (21220)
  covalent geometry    : angle       0.57856 (29080)
  hydrogen bonds       : bond        0.05177 (  910)
  hydrogen bonds       : angle       4.92323 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 254
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7697 (pm20)
REVERT: A  249 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7681 (pm20)
REVERT: B   33 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6536 (mttm)
REVERT: B  316 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6464 (tm-30)
REVERT: C   61 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7334 (ttm-80)
REVERT: C   97 ARG cc_start: 0.7104 (tpt-90) cc_final: 0.6318 (ptm160)
REVERT: C  134 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7142 (mp0)
REVERT: C  273 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.5980 (mtm180)
REVERT: C  310 ASP cc_start: 0.6869 (p0) cc_final: 0.6507 (t0)
REVERT: D   61 ARG cc_start: 0.7299 (ttm110) cc_final: 0.6712 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.6968 (tm)
REVERT: D  132 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7744 (p)
REVERT: D  290 TYR cc_start: 0.6919 (m-80) cc_final: 0.6647 (m-80)
REVERT: E   33 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7954 (ttmt)
REVERT: E   61 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7556 (tpp80)
REVERT: E  139 ARG cc_start: 0.8114 (tpt-90) cc_final: 0.7667 (ttp80)
REVERT: F   61 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7382 (ttm-80)
REVERT: F   97 ARG cc_start: 0.7104 (tpt-90) cc_final: 0.6351 (ptm160)
REVERT: F  134 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7144 (mp0)
REVERT: F  273 ARG cc_start: 0.6885 (ttp-110) cc_final: 0.5991 (mtm180)
REVERT: F  310 ASP cc_start: 0.6855 (p0) cc_final: 0.6516 (t0)
REVERT: G   61 ARG cc_start: 0.7301 (ttm110) cc_final: 0.6712 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7018 (tm)
REVERT: G  290 TYR cc_start: 0.6943 (m-80) cc_final: 0.6664 (m-80)
REVERT: H   33 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7894 (ttmt)
REVERT: H   61 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7532 (tpp80)
REVERT: H  139 ARG cc_start: 0.8107 (tpt-90) cc_final: 0.7662 (ttp80)
REVERT: I   61 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8450 (ttp-170)
REVERT: I  139 ARG cc_start: 0.8838 (tpt-90) cc_final: 0.8074 (ttp-110)
REVERT: I  236 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7668 (pm20)
REVERT: I  249 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7665 (pm20)
REVERT: J   33 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6466 (mttm)
REVERT: J  316 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6439 (tm-30)
  outliers start: 70
  outliers final: 45
  residues processed: 299
  average time/residue: 0.6405
  time to fit residues: 215.0162
Evaluate side-chains
  313 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 254
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue   33 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue  105 SER
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  159 GLU
Chi-restraints excluded: chain E residue  273 ARG
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue   61 ARG
Chi-restraints excluded: chain F residue  110 VAL
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain F residue  180 LYS
Chi-restraints excluded: chain F residue  240 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  117 LEU
Chi-restraints excluded: chain G residue  214 MET
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue  105 SER
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  159 GLU
Chi-restraints excluded: chain H residue  273 ARG
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  177 LEU
Chi-restraints excluded: chain I residue  249 GLU
Chi-restraints excluded: chain I residue  263 VAL
Chi-restraints excluded: chain I residue  271 SER
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  177 LEU
Chi-restraints excluded: chain J residue  277 ILE
Chi-restraints excluded: chain J residue  284 SER
Chi-restraints excluded: chain J residue  316 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 177 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9980
   chunk 109 optimal weight:    7.9990
   chunk 105 optimal weight:    2.9990
   chunk 246 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 202 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 192 optimal weight:    9.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
I 122 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.175610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.148164 restraints weight = 23083.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.60
r_work: 0.3530 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  21220  Z= 0.116
  Angle     :  0.530   6.430  29080  Z= 0.277
  Chirality :  0.046   0.161   3450
  Planarity :  0.006   0.049   3740
  Dihedral  :  4.594  18.869   2890
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.96 %
    Favored  : 76.42 %
  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:  0.36 (0.16), residues: 2610
  helix:  1.55 (0.19), residues: 670
  sheet:  1.13 (0.18), residues: 710
  loop : -1.08 (0.18), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 251 
 TYR   0.015   0.001   TYR E 215 
 PHE   0.015   0.001   PHE F 188 
 TRP   0.010   0.001   TRP I  52 
 HIS   0.004   0.001   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (21220)
  covalent geometry    : angle       0.52986 (29080)
  hydrogen bonds       : bond        0.04321 (  910)
  hydrogen bonds       : angle       4.69514 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 275
  time to evaluate  : 0.878 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7655 (pm20)
REVERT: A  249 GLU cc_start: 0.8355 (tp30) cc_final: 0.7484 (pm20)
REVERT: C   61 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7267 (ttm-80)
REVERT: C   97 ARG cc_start: 0.7016 (tpt-90) cc_final: 0.6151 (ptm160)
REVERT: C  128 GLN cc_start: 0.7435 (mt0) cc_final: 0.6874 (mm-40)
REVERT: C  130 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7565 (ttt180)
REVERT: C  134 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7215 (mp0)
REVERT: C  273 ARG cc_start: 0.6771 (ttp-110) cc_final: 0.5899 (mtm180)
REVERT: C  310 ASP cc_start: 0.6765 (p0) cc_final: 0.6457 (t0)
REVERT: D   61 ARG cc_start: 0.7272 (ttm110) cc_final: 0.6656 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6908 (tm)
REVERT: D  130 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7710 (tmm160)
REVERT: D  290 TYR cc_start: 0.6834 (m-80) cc_final: 0.6306 (m-80)
REVERT: E   33 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7924 (ttmt)
REVERT: E   61 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7477 (tpp80)
REVERT: E  139 ARG cc_start: 0.8002 (tpt-90) cc_final: 0.7489 (ttp80)
REVERT: F   61 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7313 (ttm-80)
REVERT: F   97 ARG cc_start: 0.7033 (tpt-90) cc_final: 0.6151 (ptm160)
REVERT: F  128 GLN cc_start: 0.7439 (mt0) cc_final: 0.6881 (mm-40)
REVERT: F  130 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7590 (ttt180)
REVERT: F  134 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7255 (mp0)
REVERT: F  273 ARG cc_start: 0.6773 (ttp-110) cc_final: 0.5921 (mtm180)
REVERT: F  310 ASP cc_start: 0.6742 (p0) cc_final: 0.6465 (t0)
REVERT: G   61 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6654 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6903 (tm)
REVERT: G  290 TYR cc_start: 0.6886 (m-80) cc_final: 0.6350 (m-80)
REVERT: H   33 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7937 (ttmt)
REVERT: H   61 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7466 (tpp80)
REVERT: H  139 ARG cc_start: 0.7993 (tpt-90) cc_final: 0.7489 (ttp80)
REVERT: I   61 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8445 (ttp-170)
REVERT: I  236 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7619 (pm20)
REVERT: I  249 GLU cc_start: 0.8370 (tp30) cc_final: 0.7522 (pm20)
REVERT: J   33 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6654 (mttp)
  outliers start: 60
  outliers final: 38
  residues processed: 314
  average time/residue: 0.7249
  time to fit residues: 254.5296
Evaluate side-chains
  304 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 258
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  273 ARG
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue   61 ARG
Chi-restraints excluded: chain F residue  110 VAL
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  117 LEU
Chi-restraints excluded: chain G residue  214 MET
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  273 ARG
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  271 SER
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  106 THR
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  277 ILE
Chi-restraints excluded: chain J residue  284 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 188 optimal weight:    5.9990
   chunk 227 optimal weight:    5.9990
   chunk 257 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 83 optimal weight:    9.9990
   chunk 107 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 141 optimal weight:    0.4980
   chunk 199 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
J 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.175714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148403 restraints weight = 23069.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.58
r_work: 0.3517 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  21220  Z= 0.119
  Angle     :  0.539   6.515  29080  Z= 0.281
  Chirality :  0.046   0.187   3450
  Planarity :  0.006   0.048   3740
  Dihedral  :  4.568  18.735   2890
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.35 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.16), residues: 2610
  helix:  1.63 (0.19), residues: 670
  sheet:  1.13 (0.18), residues: 710
  loop : -1.04 (0.18), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 251 
 TYR   0.017   0.001   TYR E 215 
 PHE   0.015   0.001   PHE C 188 
 TRP   0.010   0.001   TRP D 182 
 HIS   0.004   0.001   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (21220)
  covalent geometry    : angle       0.53923 (29080)
  hydrogen bonds       : bond        0.04405 (  910)
  hydrogen bonds       : angle       4.68913 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 263
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7756 (pm20)
REVERT: A  249 GLU cc_start: 0.8381 (tp30) cc_final: 0.7542 (pm20)
REVERT: B  316 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6494 (tm-30)
REVERT: C   61 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7389 (ttm-80)
REVERT: C   97 ARG cc_start: 0.7050 (tpt-90) cc_final: 0.6242 (ptm160)
REVERT: C  128 GLN cc_start: 0.7567 (mt0) cc_final: 0.7037 (mm-40)
REVERT: C  134 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7317 (mp0)
REVERT: C  273 ARG cc_start: 0.6862 (ttp-110) cc_final: 0.6081 (mtm180)
REVERT: C  310 ASP cc_start: 0.6800 (p0) cc_final: 0.6516 (t0)
REVERT: D   61 ARG cc_start: 0.7329 (ttm110) cc_final: 0.6721 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7014 (tm)
REVERT: D  290 TYR cc_start: 0.6897 (m-80) cc_final: 0.6488 (m-80)
REVERT: E   33 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7954 (ttmt)
REVERT: E   61 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7562 (tpp80)
REVERT: E  139 ARG cc_start: 0.8119 (tpt-90) cc_final: 0.7666 (ttp80)
REVERT: F   61 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7412 (ttm-80)
REVERT: F   97 ARG cc_start: 0.7080 (tpt-90) cc_final: 0.6250 (ptm160)
REVERT: F  128 GLN cc_start: 0.7569 (mt0) cc_final: 0.7034 (mm-40)
REVERT: F  134 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7320 (mp0)
REVERT: F  273 ARG cc_start: 0.6843 (ttp-110) cc_final: 0.6088 (mtm180)
REVERT: F  310 ASP cc_start: 0.6750 (p0) cc_final: 0.6522 (t0)
REVERT: G   61 ARG cc_start: 0.7331 (ttm110) cc_final: 0.6725 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7018 (tm)
REVERT: G  290 TYR cc_start: 0.6952 (m-80) cc_final: 0.6598 (m-80)
REVERT: H   33 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7974 (ttmt)
REVERT: H   61 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7456 (tpp80)
REVERT: H  139 ARG cc_start: 0.8111 (tpt-90) cc_final: 0.7664 (ttp80)
REVERT: I   61 ARG cc_start: 0.8703 (ttm170) cc_final: 0.8457 (ttp-170)
REVERT: I  236 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7712 (pm20)
REVERT: I  249 GLU cc_start: 0.8384 (tp30) cc_final: 0.7536 (pm20)
REVERT: J   33 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6705 (mttp)
REVERT: J  316 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6451 (tm-30)
  outliers start: 58
  outliers final: 38
  residues processed: 304
  average time/residue: 0.7256
  time to fit residues: 246.7553
Evaluate side-chains
  300 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 252
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  273 ARG
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain F residue   61 ARG
Chi-restraints excluded: chain F residue  110 VAL
Chi-restraints excluded: chain F residue  134 GLU
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  117 LEU
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  214 MET
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  273 ARG
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  177 LEU
Chi-restraints excluded: chain I residue  271 SER
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  106 THR
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  316 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 88 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 250 optimal weight:    0.9990
   chunk 222 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 208 optimal weight:    0.9980
   chunk 139 optimal weight:    5.9990
   chunk 160 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 137 optimal weight:    5.9990
   overall best weight:    0.7682

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.177268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.150111 restraints weight = 23063.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.57
r_work: 0.3530 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  21220  Z= 0.110
  Angle     :  0.526   6.112  29080  Z= 0.275
  Chirality :  0.046   0.170   3450
  Planarity :  0.006   0.048   3740
  Dihedral  :  4.465  18.230   2890
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 22.40 %
    Favored  : 75.76 %
  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:  0.53 (0.16), residues: 2610
  helix:  1.74 (0.19), residues: 670
  sheet:  1.16 (0.18), residues: 710
  loop : -0.97 (0.18), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J 251 
 TYR   0.019   0.001   TYR H 215 
 PHE   0.013   0.001   PHE C 188 
 TRP   0.009   0.001   TRP I  52 
 HIS   0.004   0.001   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (21220)
  covalent geometry    : angle       0.52559 (29080)
  hydrogen bonds       : bond        0.04070 (  910)
  hydrogen bonds       : angle       4.59800 ( 2790)

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

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

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5220 Ramachandran restraints generated.
    2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 266
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7774 (pm20)
REVERT: A  249 GLU cc_start: 0.8339 (tp30) cc_final: 0.7517 (pm20)
REVERT: B  316 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6476 (tm-30)
REVERT: C   61 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7399 (ttm-80)
REVERT: C   97 ARG cc_start: 0.7009 (tpt-90) cc_final: 0.6211 (ptm160)
REVERT: C  128 GLN cc_start: 0.7550 (mt0) cc_final: 0.7036 (mm-40)
REVERT: C  134 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7290 (mp0)
REVERT: C  273 ARG cc_start: 0.6839 (ttp-110) cc_final: 0.6092 (mtm180)
REVERT: C  310 ASP cc_start: 0.6758 (p0) cc_final: 0.6502 (t0)
REVERT: D   61 ARG cc_start: 0.7307 (ttm110) cc_final: 0.6696 (tmm-80)
REVERT: D  107 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7030 (tm)
REVERT: D  290 TYR cc_start: 0.6873 (m-80) cc_final: 0.6390 (m-80)
REVERT: E   61 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7476 (tpp80)
REVERT: E  139 ARG cc_start: 0.8096 (tpt-90) cc_final: 0.7645 (ttp80)
REVERT: F   61 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7406 (ttm-80)
REVERT: F   97 ARG cc_start: 0.7068 (tpt-90) cc_final: 0.6228 (ptm160)
REVERT: F  128 GLN cc_start: 0.7554 (mt0) cc_final: 0.7044 (mm-40)
REVERT: F  273 ARG cc_start: 0.6785 (ttp-110) cc_final: 0.6054 (mtm180)
REVERT: F  310 ASP cc_start: 0.6720 (p0) cc_final: 0.6506 (t0)
REVERT: G   61 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6691 (tmm-80)
REVERT: G  107 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7009 (tm)
REVERT: G  290 TYR cc_start: 0.6920 (m-80) cc_final: 0.6428 (m-80)
REVERT: H   33 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7989 (ttmt)
REVERT: H   61 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7557 (tpp80)
REVERT: H  139 ARG cc_start: 0.8089 (tpt-90) cc_final: 0.7637 (ttp80)
REVERT: I   61 ARG cc_start: 0.8684 (ttm170) cc_final: 0.8440 (ttp-170)
REVERT: I  236 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7716 (pm20)
REVERT: I  249 GLU cc_start: 0.8347 (tp30) cc_final: 0.7504 (pm20)
REVERT: J   33 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6636 (mttp)
REVERT: J  316 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6439 (tm-30)
  outliers start: 42
  outliers final: 25
  residues processed: 298
  average time/residue: 0.7316
  time to fit residues: 243.9377
Evaluate side-chains
  281 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 249
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  105 SER
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  273 ARG
Chi-restraints excluded: chain E residue  291 THR
Chi-restraints excluded: chain G residue  100 THR
Chi-restraints excluded: chain G residue  105 SER
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  107 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  117 LEU
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain H residue   33 LYS
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  273 ARG
Chi-restraints excluded: chain H residue  291 THR
Chi-restraints excluded: chain I residue  277 ILE
Chi-restraints excluded: chain J residue   33 LYS
Chi-restraints excluded: chain J residue  136 ILE
Chi-restraints excluded: chain J residue  316 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 260
   random chunks:
   chunk 259 optimal weight:    8.9990
   chunk 186 optimal weight:    9.9990
   chunk 174 optimal weight:    0.9990
   chunk 108 optimal weight:    6.9990
   chunk 190 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0770
   chunk 194 optimal weight:    1.9990
   chunk 209 optimal weight:    0.8980
   chunk 182 optimal weight:    6.9990
   chunk 132 optimal weight:    0.0170
   chunk 247 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN
G 146 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.178541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.151197 restraints weight = 23159.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.60
r_work: 0.3546 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  21220  Z= 0.105
  Angle     :  0.518   6.429  29080  Z= 0.269
  Chirality :  0.045   0.169   3450
  Planarity :  0.005   0.047   3740
  Dihedral  :  4.363  17.551   2890
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 22.62 %
    Favored  : 75.90 %
  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:  0.61 (0.16), residues: 2610
  helix:  1.86 (0.19), residues: 670
  sheet:  1.19 (0.18), residues: 710
  loop : -0.94 (0.18), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J 251 
 TYR   0.019   0.001   TYR H 215 
 PHE   0.012   0.001   PHE F 188 
 TRP   0.009   0.001   TRP A  52 
 HIS   0.004   0.001   HIS H 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (21220)
  covalent geometry    : angle       0.51765 (29080)
  hydrogen bonds       : bond        0.03852 (  910)
  hydrogen bonds       : angle       4.52955 ( 2790)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7770.29 seconds
wall clock time: 133 minutes 10.20 seconds (7990.20 seconds total)