Starting phenix.real_space_refine
on Thu Jul 31 11:12:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sd2_10146/07_2025/6sd2_10146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sd2_10146/07_2025/6sd2_10146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sd2_10146/07_2025/6sd2_10146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sd2_10146/07_2025/6sd2_10146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sd2_10146/07_2025/6sd2_10146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sd2_10146/07_2025/6sd2_10146.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      21      5.16       5
     C    8442      2.51       5
     N    2415      2.21       5
     O    2688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 84 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13566
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 646
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 81}
          Chain breaks: 1
  Restraints were copied for chains:
    C, b, e, D, G, F, I, c, J, L, O, N, Q, R, U, T, W, Y, Z, f
  Time building chain proxies: 5.16, per 1000 atoms: 0.38
  Number of scatterers: 13566
  At special positions: 0
  Unit cell: (166.866, 166.044, 38.634, 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      21     16.00
     O    2688      8.00
     N    2415      7.00
     C    8442      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: 3.67
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3402

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 21 sheets defined
      40.9% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA A 135 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 146 " --> pdb=" O   ARG A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'C' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA C 135 " --> pdb=" O   ASN C 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY C 138 " --> pdb=" O   ARG C 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG C 142 " --> pdb=" O   GLY C 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR C 146 " --> pdb=" O   ARG C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER C 192 " --> pdb=" O   GLU C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 208
      No H-bonds generated for 'chain 'C' and resid 206 through 208'
    Processing helix  chain 'D' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA D 135 " --> pdb=" O   ASN D 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY D 138 " --> pdb=" O   ARG D 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG D 142 " --> pdb=" O   GLY D 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR D 146 " --> pdb=" O   ARG D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 187 through 200
      removed outlier: 3.969A  pdb=" N   SER D 192 " --> pdb=" O   GLU D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'F' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA F 135 " --> pdb=" O   ASN F 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY F 138 " --> pdb=" O   ARG F 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG F 142 " --> pdb=" O   GLY F 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR F 146 " --> pdb=" O   ARG F 142 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER F 192 " --> pdb=" O   GLU F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 206 through 208
      No H-bonds generated for 'chain 'F' and resid 206 through 208'
    Processing helix  chain 'G' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA G 135 " --> pdb=" O   ASN G 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY G 138 " --> pdb=" O   ARG G 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG G 142 " --> pdb=" O   GLY G 138 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR G 146 " --> pdb=" O   ARG G 142 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER G 192 " --> pdb=" O   GLU G 188 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 206 through 208
      No H-bonds generated for 'chain 'G' and resid 206 through 208'
    Processing helix  chain 'I' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA I 135 " --> pdb=" O   ASN I 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY I 138 " --> pdb=" O   ARG I 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG I 142 " --> pdb=" O   GLY I 138 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR I 146 " --> pdb=" O   ARG I 142 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 187 through 200
      removed outlier: 3.969A  pdb=" N   SER I 192 " --> pdb=" O   GLU I 188 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 206 through 208
      No H-bonds generated for 'chain 'I' and resid 206 through 208'
    Processing helix  chain 'J' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA J 135 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY J 138 " --> pdb=" O   ARG J 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG J 142 " --> pdb=" O   GLY J 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR J 146 " --> pdb=" O   ARG J 142 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER J 192 " --> pdb=" O   GLU J 188 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 206 through 208
      No H-bonds generated for 'chain 'J' and resid 206 through 208'
    Processing helix  chain 'L' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA L 135 " --> pdb=" O   ASN L 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY L 138 " --> pdb=" O   ARG L 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG L 142 " --> pdb=" O   GLY L 138 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR L 146 " --> pdb=" O   ARG L 142 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER L 192 " --> pdb=" O   GLU L 188 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 206 through 208
      No H-bonds generated for 'chain 'L' and resid 206 through 208'
    Processing helix  chain 'N' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA N 135 " --> pdb=" O   ASN N 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY N 138 " --> pdb=" O   ARG N 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG N 142 " --> pdb=" O   GLY N 138 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR N 146 " --> pdb=" O   ARG N 142 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER N 192 " --> pdb=" O   GLU N 188 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 206 through 208
      No H-bonds generated for 'chain 'N' and resid 206 through 208'
    Processing helix  chain 'O' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA O 135 " --> pdb=" O   ASN O 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY O 138 " --> pdb=" O   ARG O 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG O 142 " --> pdb=" O   GLY O 138 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR O 146 " --> pdb=" O   ARG O 142 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER O 192 " --> pdb=" O   GLU O 188 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 206 through 208
      No H-bonds generated for 'chain 'O' and resid 206 through 208'
    Processing helix  chain 'Q' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA Q 135 " --> pdb=" O   ASN Q 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY Q 138 " --> pdb=" O   ARG Q 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG Q 142 " --> pdb=" O   GLY Q 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR Q 146 " --> pdb=" O   ARG Q 142 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER Q 192 " --> pdb=" O   GLU Q 188 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 206 through 208
      No H-bonds generated for 'chain 'Q' and resid 206 through 208'
    Processing helix  chain 'R' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA R 135 " --> pdb=" O   ASN R 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY R 138 " --> pdb=" O   ARG R 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG R 142 " --> pdb=" O   GLY R 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR R 146 " --> pdb=" O   ARG R 142 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER R 192 " --> pdb=" O   GLU R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 208
      No H-bonds generated for 'chain 'R' and resid 206 through 208'
    Processing helix  chain 'T' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA T 135 " --> pdb=" O   ASN T 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY T 138 " --> pdb=" O   ARG T 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG T 142 " --> pdb=" O   GLY T 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR T 146 " --> pdb=" O   ARG T 142 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER T 192 " --> pdb=" O   GLU T 188 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 206 through 208
      No H-bonds generated for 'chain 'T' and resid 206 through 208'
    Processing helix  chain 'U' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA U 135 " --> pdb=" O   ASN U 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY U 138 " --> pdb=" O   ARG U 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG U 142 " --> pdb=" O   GLY U 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR U 146 " --> pdb=" O   ARG U 142 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER U 192 " --> pdb=" O   GLU U 188 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 206 through 208
      No H-bonds generated for 'chain 'U' and resid 206 through 208'
    Processing helix  chain 'W' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA W 135 " --> pdb=" O   ASN W 131 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY W 138 " --> pdb=" O   ARG W 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG W 142 " --> pdb=" O   GLY W 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR W 146 " --> pdb=" O   ARG W 142 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER W 192 " --> pdb=" O   GLU W 188 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 206 through 208
      No H-bonds generated for 'chain 'W' and resid 206 through 208'
    Processing helix  chain 'Y' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA Y 135 " --> pdb=" O   ASN Y 131 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY Y 138 " --> pdb=" O   ARG Y 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG Y 142 " --> pdb=" O   GLY Y 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR Y 146 " --> pdb=" O   ARG Y 142 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 187 through 200
      removed outlier: 3.969A  pdb=" N   SER Y 192 " --> pdb=" O   GLU Y 188 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 206 through 208
      No H-bonds generated for 'chain 'Y' and resid 206 through 208'
    Processing helix  chain 'Z' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA Z 135 " --> pdb=" O   ASN Z 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY Z 138 " --> pdb=" O   ARG Z 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG Z 142 " --> pdb=" O   GLY Z 138 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR Z 146 " --> pdb=" O   ARG Z 142 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 187 through 200
      removed outlier: 3.969A  pdb=" N   SER Z 192 " --> pdb=" O   GLU Z 188 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 206 through 208
      No H-bonds generated for 'chain 'Z' and resid 206 through 208'
    Processing helix  chain 'b' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA b 135 " --> pdb=" O   ASN b 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY b 138 " --> pdb=" O   ARG b 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG b 142 " --> pdb=" O   GLY b 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR b 146 " --> pdb=" O   ARG b 142 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 187 through 200
      removed outlier: 3.969A  pdb=" N   SER b 192 " --> pdb=" O   GLU b 188 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 206 through 208
      No H-bonds generated for 'chain 'b' and resid 206 through 208'
    Processing helix  chain 'c' and resid 128 through 146
      removed outlier: 3.704A  pdb=" N   ALA c 135 " --> pdb=" O   ASN c 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY c 138 " --> pdb=" O   ARG c 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG c 142 " --> pdb=" O   GLY c 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR c 146 " --> pdb=" O   ARG c 142 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER c 192 " --> pdb=" O   GLU c 188 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 206 through 208
      No H-bonds generated for 'chain 'c' and resid 206 through 208'
    Processing helix  chain 'e' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA e 135 " --> pdb=" O   ASN e 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY e 138 " --> pdb=" O   ARG e 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG e 142 " --> pdb=" O   GLY e 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR e 146 " --> pdb=" O   ARG e 142 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 187 through 200
      removed outlier: 3.969A  pdb=" N   SER e 192 " --> pdb=" O   GLU e 188 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 206 through 208
      No H-bonds generated for 'chain 'e' and resid 206 through 208'
    Processing helix  chain 'f' and resid 128 through 146
      removed outlier: 3.703A  pdb=" N   ALA f 135 " --> pdb=" O   ASN f 131 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY f 138 " --> pdb=" O   ARG f 134 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG f 142 " --> pdb=" O   GLY f 138 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR f 146 " --> pdb=" O   ARG f 142 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 187 through 200
      removed outlier: 3.970A  pdb=" N   SER f 192 " --> pdb=" O   GLU f 188 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 206 through 208
      No H-bonds generated for 'chain 'f' and resid 206 through 208'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 158
    Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 158
    Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 158
    Processing sheet with id=AA4, first strand: chain 'F' and resid 152 through 158
    Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 158
    Processing sheet with id=AA6, first strand: chain 'I' and resid 152 through 158
    Processing sheet with id=AA7, first strand: chain 'J' and resid 152 through 158
    Processing sheet with id=AA8, first strand: chain 'L' and resid 152 through 158
    Processing sheet with id=AA9, first strand: chain 'N' and resid 152 through 158
    Processing sheet with id=AB1, first strand: chain 'O' and resid 152 through 158
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 152 through 158
    Processing sheet with id=AB3, first strand: chain 'R' and resid 152 through 158
    Processing sheet with id=AB4, first strand: chain 'T' and resid 152 through 158
    Processing sheet with id=AB5, first strand: chain 'U' and resid 152 through 158
    Processing sheet with id=AB6, first strand: chain 'W' and resid 152 through 158
    Processing sheet with id=AB7, first strand: chain 'Y' and resid 152 through 158
    Processing sheet with id=AB8, first strand: chain 'Z' and resid 152 through 158
    Processing sheet with id=AB9, first strand: chain 'b' and resid 152 through 158
    Processing sheet with id=AC1, first strand: chain 'c' and resid 152 through 158
    Processing sheet with id=AC2, first strand: chain 'e' and resid 152 through 158
    Processing sheet with id=AC3, first strand: chain 'f' and resid 152 through 158

    672 hydrogen bonds defined for protein.
    1890 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: 3.33

  Time building geometry restraints manager: 3.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4685
        1.34 -     1.46: 1832
        1.46 -     1.57: 7196
        1.57 -     1.69: 0
        1.69 -     1.80: 42
  Bond restraints: 13755
  Sorted by residual:
  bond pdb=" CA  HIS Q 218 "
       pdb=" C   HIS Q 218 "
    ideal  model  delta    sigma   weight residual
    1.532  1.518  0.014 9.60e-03 1.09e+04 2.11e+00
  bond pdb=" CA  HIS C 218 "
       pdb=" C   HIS C 218 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.014 9.60e-03 1.09e+04 2.05e+00
  bond pdb=" CA  HIS F 218 "
       pdb=" C   HIS F 218 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.014 9.60e-03 1.09e+04 2.01e+00
  bond pdb=" CA  HIS b 218 "
       pdb=" C   HIS b 218 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.014 9.60e-03 1.09e+04 1.99e+00
  bond pdb=" CA  HIS W 218 "
       pdb=" C   HIS W 218 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.013 9.60e-03 1.09e+04 1.95e+00
  ... (remaining 13750 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 15901
        1.04 -     2.08: 2070
        2.08 -     3.12: 513
        3.12 -     4.17: 185
        4.17 -     5.21: 84
  Bond angle restraints: 18753
  Sorted by residual:
  angle pdb=" N   VAL F 198 "
        pdb=" CA  VAL F 198 "
        pdb=" C   VAL F 198 "
      ideal   model   delta    sigma   weight residual
     112.12  108.68    3.44 8.40e-01 1.42e+00 1.68e+01
  angle pdb=" N   VAL U 198 "
        pdb=" CA  VAL U 198 "
        pdb=" C   VAL U 198 "
      ideal   model   delta    sigma   weight residual
     112.12  108.69    3.43 8.40e-01 1.42e+00 1.67e+01
  angle pdb=" N   VAL W 198 "
        pdb=" CA  VAL W 198 "
        pdb=" C   VAL W 198 "
      ideal   model   delta    sigma   weight residual
     112.12  108.70    3.42 8.40e-01 1.42e+00 1.66e+01
  angle pdb=" N   VAL A 198 "
        pdb=" CA  VAL A 198 "
        pdb=" C   VAL A 198 "
      ideal   model   delta    sigma   weight residual
     112.12  108.70    3.42 8.40e-01 1.42e+00 1.65e+01
  angle pdb=" N   VAL J 198 "
        pdb=" CA  VAL J 198 "
        pdb=" C   VAL J 198 "
      ideal   model   delta    sigma   weight residual
     112.12  108.71    3.41 8.40e-01 1.42e+00 1.65e+01
  ... (remaining 18748 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.35: 7082
       13.35 -    26.71: 751
       26.71 -    40.06: 399
       40.06 -    53.42: 105
       53.42 -    66.77: 63
  Dihedral angle restraints: 8400
    sinusoidal: 3171
      harmonic: 5229
  Sorted by residual:
  dihedral pdb=" CA  GLU R 128 "
           pdb=" C   GLU R 128 "
           pdb=" N   GLN R 129 "
           pdb=" CA  GLN R 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.10   18.90     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  GLU A 128 "
           pdb=" C   GLU A 128 "
           pdb=" N   GLN A 129 "
           pdb=" CA  GLN A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLU O 128 "
           pdb=" C   GLU O 128 "
           pdb=" N   GLN O 129 "
           pdb=" CA  GLN O 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 8397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1230
       0.032 -    0.064: 678
       0.064 -    0.096: 297
       0.096 -    0.128: 84
       0.128 -    0.160: 42
  Chirality restraints: 2331
  Sorted by residual:
  chirality pdb=" CB  THR U 179 "
            pdb=" CA  THR U 179 "
            pdb=" OG1 THR U 179 "
            pdb=" CG2 THR U 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CB  THR W 179 "
            pdb=" CA  THR W 179 "
            pdb=" OG1 THR W 179 "
            pdb=" CG2 THR W 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CB  THR e 179 "
            pdb=" CA  THR e 179 "
            pdb=" OG1 THR e 179 "
            pdb=" CG2 THR e 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.35e-01
  ... (remaining 2328 not shown)

  Planarity restraints: 2457
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I 179 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" C   THR I 179 "    0.022 2.00e-02 2.50e+03
        pdb=" O   THR I 179 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU I 180 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR c 179 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" C   THR c 179 "    0.022 2.00e-02 2.50e+03
        pdb=" O   THR c 179 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU c 180 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 179 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   THR C 179 "    0.022 2.00e-02 2.50e+03
        pdb=" O   THR C 179 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU C 180 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2454 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 4697
        2.86 -     3.37: 12576
        3.37 -     3.88: 21040
        3.88 -     4.39: 26350
        4.39 -     4.90: 45117
  Nonbonded interactions: 109780
  Sorted by model distance:
  nonbonded pdb=" O   THR U 146 "
            pdb=" OG1 THR U 146 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   THR I 146 "
            pdb=" OG1 THR I 146 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   THR W 146 "
            pdb=" OG1 THR W 146 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   THR A 146 "
            pdb=" OG1 THR A 146 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   THR R 146 "
            pdb=" OG1 THR R 146 "
     model   vdw
     2.355 3.040
  ... (remaining 109775 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'b'
  selection = chain 'e'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'c'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'Y'
  selection = chain 'Z'
  selection = chain 'f'
}

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:             4.620
  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:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     28.810
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.120
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
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      :  0.009   0.047  13755  Z= 0.394
  Angle     :  0.880   5.207  18753  Z= 0.514
  Chirality :  0.050   0.160   2331
  Planarity :  0.003   0.014   2457
  Dihedral  : 16.062  66.772   4998
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  :  4.17 %
    Favored  : 90.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.71 (0.17), residues: 1764
  helix: -4.00 (0.13), residues: 693
  sheet: -1.49 (0.22), residues: 504
  loop : -3.06 (0.22), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 156 
 PHE   0.007   0.002   PHE Q 126 
 TYR   0.009   0.002   TYR W 132 
 ARG   0.002   0.000   ARG c 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27936 (  672)
  hydrogen bonds       : angle       9.58882 ( 1890)
  covalent geometry    : bond        0.00862 (13755)
  covalent geometry    : angle       0.88036 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  548 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 464
  time to evaluate  : 1.397 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7934 (tttm)
REVERT: A  184 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.6763 (mtp85)
REVERT: C  151 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8088 (tttm)
REVERT: D  151 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7904 (tttm)
REVERT: F  151 LYS cc_start: 0.8577 (ttmt) cc_final: 0.7990 (tttm)
REVERT: G  151 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8076 (tttm)
REVERT: G  218 HIS cc_start: 0.7715 (m-70) cc_final: 0.7486 (m170)
REVERT: I  151 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8014 (tttm)
REVERT: J  151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7900 (tttm)
REVERT: L  139 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7165 (mm-30)
REVERT: L  151 LYS cc_start: 0.8555 (ttmt) cc_final: 0.7835 (tttm)
REVERT: N  151 LYS cc_start: 0.8563 (ttmt) cc_final: 0.7916 (tttm)
REVERT: O  134 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7716 (ttp-170)
REVERT: O  139 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7224 (mm-30)
REVERT: O  151 LYS cc_start: 0.8645 (ttmt) cc_final: 0.7950 (tttm)
REVERT: O  218 HIS cc_start: 0.7659 (m-70) cc_final: 0.7426 (m170)
REVERT: Q  151 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8066 (tttm)
REVERT: R  151 LYS cc_start: 0.8547 (ttmt) cc_final: 0.7868 (tttm)
REVERT: R  184 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.6790 (mtp85)
REVERT: R  218 HIS cc_start: 0.7724 (m-70) cc_final: 0.7504 (m170)
REVERT: T  134 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7707 (ttp-170)
REVERT: T  151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7870 (tttm)
REVERT: T  197 LEU cc_start: 0.8504 (tp) cc_final: 0.8262 (tt)
REVERT: U  151 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7809 (tttm)
REVERT: W  151 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7895 (tttm)
REVERT: Y  151 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7978 (tttm)
REVERT: Z  151 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7851 (tttm)
REVERT: Z  184 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.6683 (mtp85)
REVERT: b  151 LYS cc_start: 0.8571 (ttmt) cc_final: 0.7858 (tttm)
REVERT: b  177 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8110 (m)
REVERT: b  218 HIS cc_start: 0.7752 (m-70) cc_final: 0.7547 (m170)
REVERT: c  151 LYS cc_start: 0.8538 (ttmt) cc_final: 0.7934 (tttm)
REVERT: c  218 HIS cc_start: 0.7781 (m-70) cc_final: 0.7563 (m170)
REVERT: e  151 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8022 (tttm)
REVERT: f  151 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8072 (tttm)
  outliers start: 84
  outliers final: 25
  residues processed: 494
  average time/residue: 0.3168
  time to fit residues: 208.8191
Evaluate side-chains
  397 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 369
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain C residue  139 GLU
Chi-restraints excluded: chain D residue  139 GLU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain F residue  139 GLU
Chi-restraints excluded: chain F residue  177 THR
Chi-restraints excluded: chain G residue  139 GLU
Chi-restraints excluded: chain I residue  139 GLU
Chi-restraints excluded: chain I residue  177 THR
Chi-restraints excluded: chain J residue  139 GLU
Chi-restraints excluded: chain L residue  139 GLU
Chi-restraints excluded: chain N residue  139 GLU
Chi-restraints excluded: chain O residue  139 GLU
Chi-restraints excluded: chain Q residue  139 GLU
Chi-restraints excluded: chain Q residue  177 THR
Chi-restraints excluded: chain R residue  139 GLU
Chi-restraints excluded: chain T residue  139 GLU
Chi-restraints excluded: chain U residue  139 GLU
Chi-restraints excluded: chain W residue  139 GLU
Chi-restraints excluded: chain Y residue  139 GLU
Chi-restraints excluded: chain Z residue  139 GLU
Chi-restraints excluded: chain b residue  139 GLU
Chi-restraints excluded: chain b residue  177 THR
Chi-restraints excluded: chain c residue  139 GLU
Chi-restraints excluded: chain e residue  139 GLU
Chi-restraints excluded: chain f residue  139 GLU
Chi-restraints excluded: chain f residue  177 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.3980
   chunk 127 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   chunk 80 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0980
   chunk 152 optimal weight:    1.9990
   overall best weight:    0.2338

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
C 196 HIS
D 196 HIS
F 196 HIS
G 196 HIS
I 196 HIS
J 196 HIS
L 196 HIS
N 196 HIS
O 196 HIS
Q 196 HIS
R 196 HIS
T 196 HIS
U 190 GLN
U 196 HIS
W 196 HIS
Y 196 HIS
Z 196 HIS
b 196 HIS
c 196 HIS
e 196 HIS
f 196 HIS

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.138958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.113566 restraints weight = 15746.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.39
r_work: 0.3065 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13755  Z= 0.122
  Angle     :  0.613   8.871  18753  Z= 0.301
  Chirality :  0.042   0.126   2331
  Planarity :  0.004   0.030   2457
  Dihedral  :  5.494  31.225   1981
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.53 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.20), residues: 1764
  helix: -2.34 (0.15), residues: 714
  sheet:  0.47 (0.27), residues: 462
  loop : -2.20 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS Y 156 
 PHE   0.001   0.000   PHE b 126 
 TYR   0.011   0.001   TYR F 132 
 ARG   0.003   0.001   ARG U 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04198 (  672)
  hydrogen bonds       : angle       5.22357 ( 1890)
  covalent geometry    : bond        0.00290 (13755)
  covalent geometry    : angle       0.61310 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  436 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 426
  time to evaluate  : 1.595 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8003 (tttm)
REVERT: A  184 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.6839 (mtp85)
REVERT: A  188 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7885 (mt-10)
REVERT: C  131 ASN cc_start: 0.7949 (t0) cc_final: 0.7687 (t0)
REVERT: C  151 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8096 (tttm)
REVERT: C  184 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.6860 (mtp85)
REVERT: D  131 ASN cc_start: 0.8036 (t0) cc_final: 0.7712 (t0)
REVERT: D  151 LYS cc_start: 0.8514 (ttmt) cc_final: 0.7989 (tttm)
REVERT: F  131 ASN cc_start: 0.7889 (t0) cc_final: 0.7663 (t0)
REVERT: F  151 LYS cc_start: 0.8585 (ttmt) cc_final: 0.7983 (tttm)
REVERT: F  152 SER cc_start: 0.9184 (p) cc_final: 0.8963 (p)
REVERT: F  222 GLN cc_start: 0.6183 (mm110) cc_final: 0.5928 (mm110)
REVERT: G  142 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7681 (mtm110)
REVERT: G  151 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8156 (tttm)
REVERT: I  151 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8087 (tttm)
REVERT: J  151 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8129 (tttm)
REVERT: L  131 ASN cc_start: 0.7874 (t0) cc_final: 0.7548 (t0)
REVERT: L  151 LYS cc_start: 0.8600 (ttmt) cc_final: 0.7897 (tttm)
REVERT: L  173 SER cc_start: 0.8459 (p) cc_final: 0.8208 (m)
REVERT: N  151 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8025 (tttm)
REVERT: O  134 ARG cc_start: 0.8435 (mtp180) cc_final: 0.8220 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8046 (tttm)
REVERT: Q  151 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8080 (tttm)
REVERT: R  142 ARG cc_start: 0.7994 (mmt-90) cc_final: 0.7783 (mtm110)
REVERT: R  151 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8002 (tttm)
REVERT: T  151 LYS cc_start: 0.8597 (ttmt) cc_final: 0.7947 (tttm)
REVERT: U  142 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.7743 (mtm110)
REVERT: U  151 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8076 (tttm)
REVERT: W  151 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8025 (tttm)
REVERT: Y  151 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8035 (tttm)
REVERT: Z  151 LYS cc_start: 0.8560 (ttmt) cc_final: 0.7910 (tttm)
REVERT: Z  184 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.6809 (mtp85)
REVERT: b  151 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8026 (tttm)
REVERT: c  151 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8003 (tttm)
REVERT: e  151 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8087 (tttm)
REVERT: e  216 SER cc_start: 0.8915 (m) cc_final: 0.8700 (p)
REVERT: f  151 LYS cc_start: 0.8540 (ttmt) cc_final: 0.7972 (tttm)
REVERT: f  184 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.6730 (mtp85)
  outliers start: 10
  outliers final: 5
  residues processed: 434
  average time/residue: 0.3791
  time to fit residues: 215.6203
Evaluate side-chains
  347 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 342
  time to evaluate  : 1.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain b residue  180 LEU
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 105 optimal weight:    0.1980
   chunk 108 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 140 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 55 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
F 190 GLN
G 190 GLN
J 190 GLN
L 190 GLN
O 190 GLN
O 218 HIS
U 190 GLN
W 190 GLN
b 190 GLN
e 190 GLN
f 190 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.132954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.107766 restraints weight = 16044.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.35
r_work: 0.3023 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13755  Z= 0.151
  Angle     :  0.592   9.534  18753  Z= 0.285
  Chirality :  0.043   0.118   2331
  Planarity :  0.004   0.032   2457
  Dihedral  :  4.557  13.728   1911
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.12 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.22), residues: 1764
  helix: -1.19 (0.19), residues: 651
  sheet:  0.26 (0.25), residues: 504
  loop : -1.26 (0.31), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J 156 
 PHE   0.003   0.001   PHE b 126 
 TYR   0.008   0.001   TYR F 132 
 ARG   0.006   0.001   ARG R 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  672)
  hydrogen bonds       : angle       4.77485 ( 1890)
  covalent geometry    : bond        0.00379 (13755)
  covalent geometry    : angle       0.59162 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 335
  time to evaluate  : 1.637 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8043 (tttm)
REVERT: A  154 ARG cc_start: 0.8909 (mtp-110) cc_final: 0.8645 (mtp85)
REVERT: A  184 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.6890 (mtp85)
REVERT: C  131 ASN cc_start: 0.7898 (t0) cc_final: 0.7651 (t0)
REVERT: C  151 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8185 (tttm)
REVERT: C  184 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.6891 (mtp85)
REVERT: C  188 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: D  131 ASN cc_start: 0.7994 (t0) cc_final: 0.7720 (t0)
REVERT: D  151 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7973 (tttm)
REVERT: F  131 ASN cc_start: 0.7972 (t0) cc_final: 0.7749 (t0)
REVERT: F  151 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8098 (tttm)
REVERT: F  152 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8914 (p)
REVERT: F  222 GLN cc_start: 0.6356 (mm110) cc_final: 0.6110 (mm110)
REVERT: G  151 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8206 (tttm)
REVERT: I  151 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8197 (tttm)
REVERT: J  151 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8137 (tttm)
REVERT: L  131 ASN cc_start: 0.7784 (t0) cc_final: 0.7489 (t0)
REVERT: L  151 LYS cc_start: 0.8581 (ttmt) cc_final: 0.7964 (tttm)
REVERT: N  142 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7592 (mtt90)
REVERT: N  151 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8040 (tttm)
REVERT: O  134 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8122 (ttp-110)
REVERT: O  142 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7439 (mtt90)
REVERT: O  151 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8052 (tttm)
REVERT: Q  151 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8103 (tttm)
REVERT: R  151 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8021 (tttm)
REVERT: T  151 LYS cc_start: 0.8560 (ttmt) cc_final: 0.7941 (tttm)
REVERT: U  151 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8115 (tttm)
REVERT: U  188 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7705 (mt-10)
REVERT: W  151 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8014 (tttm)
REVERT: Y  151 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8131 (tttm)
REVERT: Z  151 LYS cc_start: 0.8585 (ttmt) cc_final: 0.7961 (tttm)
REVERT: Z  184 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.6812 (mtp85)
REVERT: b  151 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8077 (tttm)
REVERT: c  151 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8021 (tttm)
REVERT: e  151 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8083 (tttm)
REVERT: e  216 SER cc_start: 0.8928 (m) cc_final: 0.8724 (p)
REVERT: f  151 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8021 (tttm)
REVERT: f  184 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.6856 (mtp85)
  outliers start: 41
  outliers final: 25
  residues processed: 367
  average time/residue: 0.4883
  time to fit residues: 230.5884
Evaluate side-chains
  347 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 321
  time to evaluate  : 2.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain F residue  152 SER
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  173 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 124 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 143 optimal weight:    2.9990
   chunk 155 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
F 190 GLN
G 190 GLN
L 190 GLN
U 190 GLN
b 190 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.134233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.108486 restraints weight = 15826.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.38
r_work: 0.3020 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13755  Z= 0.166
  Angle     :  0.577   9.073  18753  Z= 0.278
  Chirality :  0.043   0.119   2331
  Planarity :  0.003   0.026   2457
  Dihedral  :  4.466  13.168   1911
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  :  9.92 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.22), residues: 1764
  helix: -1.22 (0.18), residues: 714
  sheet:  0.41 (0.24), residues: 504
  loop : -1.49 (0.34), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 156 
 PHE   0.004   0.001   PHE b 126 
 TYR   0.010   0.001   TYR F 132 
 ARG   0.007   0.000   ARG Q 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  672)
  hydrogen bonds       : angle       4.55257 ( 1890)
  covalent geometry    : bond        0.00407 (13755)
  covalent geometry    : angle       0.57684 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 322
  time to evaluate  : 1.659 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7970 (tttm)
REVERT: A  154 ARG cc_start: 0.8830 (mtp-110) cc_final: 0.8610 (mtp85)
REVERT: C  131 ASN cc_start: 0.7942 (t0) cc_final: 0.7698 (t0)
REVERT: C  151 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8167 (tttm)
REVERT: D  151 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7943 (tttm)
REVERT: F  131 ASN cc_start: 0.7942 (t0) cc_final: 0.7680 (t0)
REVERT: F  151 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8070 (tttm)
REVERT: G  151 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8144 (tttm)
REVERT: I  151 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8091 (tttm)
REVERT: J  151 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8128 (tttm)
REVERT: L  131 ASN cc_start: 0.7751 (t0) cc_final: 0.7493 (t0)
REVERT: L  151 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8003 (tttm)
REVERT: N  151 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8101 (tttm)
REVERT: O  134 ARG cc_start: 0.8393 (mtp180) cc_final: 0.8188 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8089 (tttm)
REVERT: Q  151 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8000 (tttm)
REVERT: Q  184 ARG cc_start: 0.7567 (mtt90) cc_final: 0.6598 (mtp85)
REVERT: R  151 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8025 (tttm)
REVERT: T  142 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7483 (mtt90)
REVERT: T  151 LYS cc_start: 0.8427 (ttmt) cc_final: 0.7835 (tttm)
REVERT: U  142 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7786 (mmt-90)
REVERT: U  151 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8031 (tttm)
REVERT: W  151 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8045 (tttm)
REVERT: Y  151 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8054 (tttm)
REVERT: Y  222 GLN cc_start: 0.6161 (mm110) cc_final: 0.5858 (mm110)
REVERT: Z  151 LYS cc_start: 0.8588 (ttmt) cc_final: 0.7950 (tttm)
REVERT: b  151 LYS cc_start: 0.8605 (ttmt) cc_final: 0.7929 (tttm)
REVERT: c  151 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8033 (tttm)
REVERT: e  151 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8113 (tttm)
REVERT: f  151 LYS cc_start: 0.8537 (ttmt) cc_final: 0.7965 (tttm)
  outliers start: 35
  outliers final: 31
  residues processed: 346
  average time/residue: 0.3948
  time to fit residues: 174.9690
Evaluate side-chains
  344 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 313
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  130 VAL
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  173 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 166 optimal weight:    0.6980
   chunk 146 optimal weight:    0.0670
   chunk 163 optimal weight:    1.9990
   chunk 152 optimal weight:    1.9990
   chunk 106 optimal weight:    0.4980
   chunk 128 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 167 optimal weight:    0.8980
   chunk 85 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
G 190 GLN
L 190 GLN
U 190 GLN
b 190 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.137190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.111350 restraints weight = 15832.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.40
r_work: 0.3053 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13755  Z= 0.108
  Angle     :  0.526   8.036  18753  Z= 0.253
  Chirality :  0.042   0.132   2331
  Planarity :  0.003   0.020   2457
  Dihedral  :  4.181  12.870   1911
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.58 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.22), residues: 1764
  helix: -0.68 (0.18), residues: 714
  sheet:  0.71 (0.24), residues: 504
  loop : -1.25 (0.35), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 156 
 PHE   0.002   0.001   PHE T 126 
 TYR   0.010   0.001   TYR F 132 
 ARG   0.005   0.000   ARG Q 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (  672)
  hydrogen bonds       : angle       4.12954 ( 1890)
  covalent geometry    : bond        0.00278 (13755)
  covalent geometry    : angle       0.52568 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 312
  time to evaluate  : 1.640 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7883 (tttm)
REVERT: C  151 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8100 (tttm)
REVERT: D  151 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7990 (tttm)
REVERT: F  151 LYS cc_start: 0.8449 (ttmt) cc_final: 0.7942 (tttm)
REVERT: G  151 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8049 (tttm)
REVERT: I  151 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8101 (tttm)
REVERT: J  151 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8155 (tttm)
REVERT: L  131 ASN cc_start: 0.7581 (t0) cc_final: 0.7320 (t0)
REVERT: L  151 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8016 (tttm)
REVERT: N  151 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7984 (tttm)
REVERT: O  134 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7925 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8043 (tttm)
REVERT: Q  151 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8009 (tttm)
REVERT: Q  184 ARG cc_start: 0.7569 (mtt90) cc_final: 0.6616 (mtp85)
REVERT: R  151 LYS cc_start: 0.8513 (ttmt) cc_final: 0.7862 (tttm)
REVERT: T  151 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7822 (tttm)
REVERT: U  151 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8106 (tttm)
REVERT: W  151 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8017 (tttm)
REVERT: Y  151 LYS cc_start: 0.8572 (ttmt) cc_final: 0.7999 (tttm)
REVERT: Y  222 GLN cc_start: 0.6152 (mm110) cc_final: 0.5846 (mm110)
REVERT: Z  151 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7864 (tttm)
REVERT: b  151 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7891 (tttm)
REVERT: c  151 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8042 (tttm)
REVERT: e  151 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8058 (tttm)
REVERT: f  151 LYS cc_start: 0.8474 (ttmt) cc_final: 0.7915 (tttm)
  outliers start: 36
  outliers final: 31
  residues processed: 335
  average time/residue: 0.4775
  time to fit residues: 204.6985
Evaluate side-chains
  328 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 297
  time to evaluate  : 2.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  173 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain b residue  180 LEU
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain c residue  180 LEU
Chi-restraints excluded: chain e residue  173 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 134 optimal weight:    0.0870
   chunk 84 optimal weight:    3.9990
   chunk 109 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7958

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

Flipped N/Q/H residues before XYZ refinement:
F 190 GLN
G 190 GLN
e 218 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.133226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.107644 restraints weight = 16068.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.39
r_work: 0.3022 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13755  Z= 0.155
  Angle     :  0.543   7.988  18753  Z= 0.260
  Chirality :  0.043   0.119   2331
  Planarity :  0.003   0.018   2457
  Dihedral  :  4.182  12.712   1911
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 11.77 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.22), residues: 1764
  helix: -0.50 (0.18), residues: 735
  sheet:  0.76 (0.23), residues: 504
  loop : -1.00 (0.36), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 196 
 PHE   0.004   0.001   PHE c 126 
 TYR   0.010   0.001   TYR F 132 
 ARG   0.004   0.000   ARG Q 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  672)
  hydrogen bonds       : angle       4.25001 ( 1890)
  covalent geometry    : bond        0.00384 (13755)
  covalent geometry    : angle       0.54271 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 309
  time to evaluate  : 1.442 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7906 (tttm)
REVERT: C  151 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8139 (tttm)
REVERT: D  151 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8008 (tttm)
REVERT: F  151 LYS cc_start: 0.8491 (ttmt) cc_final: 0.7947 (tttm)
REVERT: G  151 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8123 (tttm)
REVERT: I  151 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8120 (tttm)
REVERT: J  151 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8156 (tttm)
REVERT: L  131 ASN cc_start: 0.7663 (t0) cc_final: 0.7404 (t0)
REVERT: L  151 LYS cc_start: 0.8598 (ttmt) cc_final: 0.7980 (tttm)
REVERT: N  151 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8017 (tttm)
REVERT: O  134 ARG cc_start: 0.8352 (mtp180) cc_final: 0.8035 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8052 (tttm)
REVERT: Q  151 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8002 (tttm)
REVERT: R  151 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7880 (tttm)
REVERT: T  151 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7864 (tttm)
REVERT: U  151 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8139 (tttm)
REVERT: W  151 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7990 (tttm)
REVERT: Y  151 LYS cc_start: 0.8590 (ttmt) cc_final: 0.7998 (tttm)
REVERT: Y  222 GLN cc_start: 0.6283 (mm110) cc_final: 0.6013 (mm110)
REVERT: Z  131 ASN cc_start: 0.7965 (t0) cc_final: 0.7710 (m-40)
REVERT: Z  151 LYS cc_start: 0.8498 (ttmt) cc_final: 0.7931 (tttm)
REVERT: b  151 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7901 (tttm)
REVERT: c  151 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8060 (tttm)
REVERT: e  151 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8073 (tttm)
REVERT: f  151 LYS cc_start: 0.8530 (ttmt) cc_final: 0.7939 (tttm)
  outliers start: 38
  outliers final: 34
  residues processed: 333
  average time/residue: 0.4084
  time to fit residues: 173.5696
Evaluate side-chains
  338 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 304
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  173 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  173 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain c residue  180 LEU
Chi-restraints excluded: chain e residue  173 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  173 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 148 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 165 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 136 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
G 190 GLN
e 218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.134643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.108609 restraints weight = 15847.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.42
r_work: 0.3002 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13755  Z= 0.172
  Angle     :  0.551   7.696  18753  Z= 0.266
  Chirality :  0.043   0.129   2331
  Planarity :  0.003   0.021   2457
  Dihedral  :  4.223  12.771   1911
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.37 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.22), residues: 1764
  helix: -0.31 (0.18), residues: 735
  sheet:  0.71 (0.23), residues: 504
  loop : -0.93 (0.36), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS e 218 
 PHE   0.005   0.002   PHE c 126 
 TYR   0.011   0.001   TYR F 132 
 ARG   0.003   0.000   ARG Q 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  672)
  hydrogen bonds       : angle       4.28695 ( 1890)
  covalent geometry    : bond        0.00418 (13755)
  covalent geometry    : angle       0.55147 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 314
  time to evaluate  : 1.684 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7910 (tttm)
REVERT: C  151 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8129 (tttm)
REVERT: D  151 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7998 (tttm)
REVERT: F  131 ASN cc_start: 0.7903 (t0) cc_final: 0.7677 (t0)
REVERT: F  151 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8033 (tttm)
REVERT: G  151 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8124 (tttm)
REVERT: I  151 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8106 (tttm)
REVERT: J  151 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8117 (tttm)
REVERT: L  131 ASN cc_start: 0.7743 (t0) cc_final: 0.7497 (t0)
REVERT: L  151 LYS cc_start: 0.8564 (ttmt) cc_final: 0.7950 (tttm)
REVERT: N  151 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8018 (tttm)
REVERT: O  151 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8035 (tttm)
REVERT: Q  151 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8049 (tttm)
REVERT: R  151 LYS cc_start: 0.8542 (ttmt) cc_final: 0.7864 (tttm)
REVERT: T  151 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7839 (tttm)
REVERT: U  151 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8137 (tttm)
REVERT: W  151 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8018 (tttm)
REVERT: Y  151 LYS cc_start: 0.8575 (ttmt) cc_final: 0.7973 (tttm)
REVERT: Y  222 GLN cc_start: 0.6263 (mm110) cc_final: 0.5985 (mm110)
REVERT: Z  131 ASN cc_start: 0.7909 (t0) cc_final: 0.7616 (m-40)
REVERT: Z  151 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7912 (tttm)
REVERT: b  151 LYS cc_start: 0.8503 (ttmt) cc_final: 0.7888 (tttm)
REVERT: c  151 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8037 (tttm)
REVERT: e  151 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8063 (tttm)
REVERT: f  151 LYS cc_start: 0.8559 (ttmt) cc_final: 0.7963 (tttm)
  outliers start: 36
  outliers final: 32
  residues processed: 336
  average time/residue: 0.4002
  time to fit residues: 171.4393
Evaluate side-chains
  343 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 311
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  173 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain c residue  180 LEU
Chi-restraints excluded: chain e residue  173 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  173 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 133 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
F 190 GLN
G 190 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.135022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.108927 restraints weight = 15911.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.43
r_work: 0.3010 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13755  Z= 0.152
  Angle     :  0.537   7.413  18753  Z= 0.259
  Chirality :  0.043   0.120   2331
  Planarity :  0.003   0.018   2457
  Dihedral  :  4.171  12.781   1911
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.57 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.22), residues: 1764
  helix: -0.07 (0.18), residues: 735
  sheet:  0.71 (0.23), residues: 504
  loop : -0.91 (0.35), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS c 196 
 PHE   0.004   0.001   PHE U 126 
 TYR   0.010   0.001   TYR F 132 
 ARG   0.004   0.000   ARG Q 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  672)
  hydrogen bonds       : angle       4.19432 ( 1890)
  covalent geometry    : bond        0.00376 (13755)
  covalent geometry    : angle       0.53749 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 307
  time to evaluate  : 1.417 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7892 (tttm)
REVERT: C  151 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8099 (tttm)
REVERT: D  151 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7998 (tttm)
REVERT: F  151 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8017 (tttm)
REVERT: G  151 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8073 (tttm)
REVERT: I  151 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8099 (tttm)
REVERT: J  151 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8087 (tttm)
REVERT: L  131 ASN cc_start: 0.7733 (t0) cc_final: 0.7497 (t0)
REVERT: L  151 LYS cc_start: 0.8556 (ttmt) cc_final: 0.7947 (tttm)
REVERT: L  188 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7310 (mt-10)
REVERT: N  151 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8003 (tttm)
REVERT: O  134 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7863 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8025 (tttm)
REVERT: Q  151 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8003 (tttm)
REVERT: R  151 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7947 (tttm)
REVERT: T  151 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7863 (tttm)
REVERT: U  151 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8129 (tttm)
REVERT: W  151 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8003 (tttm)
REVERT: Y  151 LYS cc_start: 0.8573 (ttmt) cc_final: 0.7971 (tttm)
REVERT: Y  222 GLN cc_start: 0.6253 (mm110) cc_final: 0.5981 (mm110)
REVERT: Z  131 ASN cc_start: 0.7877 (t0) cc_final: 0.7579 (m-40)
REVERT: Z  151 LYS cc_start: 0.8435 (ttmt) cc_final: 0.7876 (tttm)
REVERT: b  151 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7903 (tttm)
REVERT: c  151 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8035 (tttm)
REVERT: e  151 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8057 (tttm)
REVERT: f  151 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7958 (tttm)
  outliers start: 34
  outliers final: 33
  residues processed: 328
  average time/residue: 0.4162
  time to fit residues: 173.8608
Evaluate side-chains
  339 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 306
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  173 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain c residue  180 LEU
Chi-restraints excluded: chain e residue  173 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  173 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 158 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0470
   chunk 151 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
G 190 GLN
e 218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.137388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.111527 restraints weight = 15738.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.42
r_work: 0.3046 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13755  Z= 0.107
  Angle     :  0.508   6.994  18753  Z= 0.244
  Chirality :  0.042   0.125   2331
  Planarity :  0.003   0.018   2457
  Dihedral  :  4.036  12.571   1911
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.70 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.22), residues: 1764
  helix:  0.53 (0.18), residues: 735
  sheet:  0.79 (0.23), residues: 504
  loop : -0.90 (0.35), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS e 218 
 PHE   0.002   0.001   PHE U 126 
 TYR   0.011   0.001   TYR F 132 
 ARG   0.003   0.000   ARG Q 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  672)
  hydrogen bonds       : angle       3.89244 ( 1890)
  covalent geometry    : bond        0.00278 (13755)
  covalent geometry    : angle       0.50785 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 302
  time to evaluate  : 1.592 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7881 (tttm)
REVERT: C  151 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8096 (tttm)
REVERT: C  154 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8324 (mtp85)
REVERT: D  151 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7957 (tttm)
REVERT: F  151 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7950 (tttm)
REVERT: G  151 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8008 (tttm)
REVERT: I  151 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8057 (tttm)
REVERT: J  151 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8017 (tttm)
REVERT: L  131 ASN cc_start: 0.7624 (t0) cc_final: 0.7397 (t0)
REVERT: L  151 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7879 (tttm)
REVERT: N  151 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7971 (tttm)
REVERT: O  134 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7748 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8573 (ttmt) cc_final: 0.7990 (tttm)
REVERT: Q  151 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8074 (tttm)
REVERT: R  151 LYS cc_start: 0.8459 (ttmt) cc_final: 0.7874 (tttm)
REVERT: T  151 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7863 (tttm)
REVERT: U  151 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8044 (tttm)
REVERT: W  151 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7973 (tttm)
REVERT: Y  151 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7936 (tttm)
REVERT: Y  222 GLN cc_start: 0.6225 (mm110) cc_final: 0.5965 (mm110)
REVERT: Z  151 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7832 (tttm)
REVERT: b  151 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7911 (tttm)
REVERT: c  151 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8001 (tttm)
REVERT: e  151 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8046 (tttm)
REVERT: f  151 LYS cc_start: 0.8535 (ttmt) cc_final: 0.7953 (tttm)
  outliers start: 37
  outliers final: 32
  residues processed: 324
  average time/residue: 0.4230
  time to fit residues: 173.8066
Evaluate side-chains
  331 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 299
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  173 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain c residue  180 LEU
Chi-restraints excluded: chain e residue  173 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  173 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 113 optimal weight:    0.5980
   chunk 47 optimal weight:    5.9990
   chunk 131 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 150 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
F 190 GLN
G 190 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.136173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.110528 restraints weight = 15740.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.36
r_work: 0.3022 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13755  Z= 0.139
  Angle     :  0.527   7.199  18753  Z= 0.253
  Chirality :  0.043   0.142   2331
  Planarity :  0.003   0.027   2457
  Dihedral  :  4.073  12.380   1911
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.96 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.22), residues: 1764
  helix:  0.58 (0.18), residues: 735
  sheet:  0.82 (0.23), residues: 504
  loop : -0.90 (0.35), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS e 218 
 PHE   0.004   0.001   PHE D 126 
 TYR   0.012   0.001   TYR F 132 
 ARG   0.006   0.000   ARG U 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  672)
  hydrogen bonds       : angle       4.00713 ( 1890)
  covalent geometry    : bond        0.00350 (13755)
  covalent geometry    : angle       0.52733 (18753)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 297
  time to evaluate  : 1.472 
Fit side-chains
REVERT: A  151 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7910 (tttm)
REVERT: C  151 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8106 (tttm)
REVERT: D  151 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7987 (tttm)
REVERT: F  151 LYS cc_start: 0.8503 (ttmt) cc_final: 0.7967 (tttm)
REVERT: G  151 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8062 (tttm)
REVERT: I  151 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8127 (tttm)
REVERT: J  151 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8053 (tttm)
REVERT: L  131 ASN cc_start: 0.7672 (t0) cc_final: 0.7455 (t0)
REVERT: L  151 LYS cc_start: 0.8536 (ttmt) cc_final: 0.7923 (tttm)
REVERT: N  151 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8019 (tttm)
REVERT: O  134 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7973 (ttp-170)
REVERT: O  151 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8041 (tttm)
REVERT: Q  151 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8064 (tttm)
REVERT: R  151 LYS cc_start: 0.8461 (ttmt) cc_final: 0.7869 (tttm)
REVERT: T  151 LYS cc_start: 0.8391 (ttmt) cc_final: 0.7874 (tttm)
REVERT: U  151 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8045 (tttm)
REVERT: W  151 LYS cc_start: 0.8559 (ttmt) cc_final: 0.7982 (tttm)
REVERT: Y  151 LYS cc_start: 0.8531 (ttmt) cc_final: 0.7993 (tttm)
REVERT: Y  222 GLN cc_start: 0.6372 (mm110) cc_final: 0.6129 (mm110)
REVERT: Z  151 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7888 (tttm)
REVERT: b  151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7941 (tttm)
REVERT: c  151 LYS cc_start: 0.8469 (ttmt) cc_final: 0.7995 (tttm)
REVERT: e  151 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8076 (tttm)
REVERT: f  151 LYS cc_start: 0.8566 (ttmt) cc_final: 0.7959 (tttm)
  outliers start: 34
  outliers final: 33
  residues processed: 316
  average time/residue: 0.4508
  time to fit residues: 179.8689
Evaluate side-chains
  330 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 297
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain C residue  173 SER
Chi-restraints excluded: chain C residue  175 SER
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain F residue  173 SER
Chi-restraints excluded: chain F residue  175 SER
Chi-restraints excluded: chain G residue  175 SER
Chi-restraints excluded: chain G residue  180 LEU
Chi-restraints excluded: chain I residue  175 SER
Chi-restraints excluded: chain J residue  175 SER
Chi-restraints excluded: chain L residue  173 SER
Chi-restraints excluded: chain L residue  175 SER
Chi-restraints excluded: chain N residue  175 SER
Chi-restraints excluded: chain O residue  175 SER
Chi-restraints excluded: chain Q residue  175 SER
Chi-restraints excluded: chain R residue  159 MET
Chi-restraints excluded: chain R residue  173 SER
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain W residue  175 SER
Chi-restraints excluded: chain Y residue  175 SER
Chi-restraints excluded: chain Z residue  173 SER
Chi-restraints excluded: chain Z residue  175 SER
Chi-restraints excluded: chain b residue  173 SER
Chi-restraints excluded: chain b residue  175 SER
Chi-restraints excluded: chain c residue  173 SER
Chi-restraints excluded: chain c residue  175 SER
Chi-restraints excluded: chain c residue  180 LEU
Chi-restraints excluded: chain e residue  173 SER
Chi-restraints excluded: chain e residue  175 SER
Chi-restraints excluded: chain f residue  173 SER
Chi-restraints excluded: chain f residue  175 SER
Chi-restraints excluded: chain f residue  179 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    0.4980
   chunk 143 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
G 190 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.135513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109679 restraints weight = 15946.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.38
r_work: 0.3019 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13755  Z= 0.160
  Angle     :  0.539   7.218  18753  Z= 0.259
  Chirality :  0.043   0.135   2331
  Planarity :  0.003   0.026   2457
  Dihedral  :  4.143  12.602   1911
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.23 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.21), residues: 1764
  helix:  0.46 (0.18), residues: 735
  sheet:  0.84 (0.23), residues: 504
  loop : -0.88 (0.35), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS e 218 
 PHE   0.004   0.001   PHE c 126 
 TYR   0.013   0.001   TYR F 132 
 ARG   0.006   0.000   ARG U 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03324 (  672)
  hydrogen bonds       : angle       4.10024 ( 1890)
  covalent geometry    : bond        0.00394 (13755)
  covalent geometry    : angle       0.53937 (18753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7561.29 seconds
wall clock time: 134 minutes 9.18 seconds (8049.18 seconds total)