Starting phenix.real_space_refine
on Thu Mar  5 06:43:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pkp_13476/03_2026/7pkp_13476.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pkp_13476/03_2026/7pkp_13476.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/7pkp_13476/03_2026/7pkp_13476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pkp_13476/03_2026/7pkp_13476.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pkp_13476/03_2026/7pkp_13476.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pkp_13476/03_2026/7pkp_13476.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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     120      5.16       5
     C   13064      2.51       5
     N    3456      2.21       5
     O    3720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20360
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "U"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "A"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "B"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "C"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "D"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "E"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "F"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
    Chain: "G"
      Number of atoms: 2545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2545
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
  Time building chain proxies: 3.86, per 1000 atoms: 0.19
  Number of scatterers: 20360
  At special positions: 0
  Unit cell: (133.75, 133.75, 108.07, 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     120     16.00
     O    3720      8.00
     N    3456      7.00
     C   13064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 823.3 milliseconds
  

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4848

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 24 sheets defined
      43.1% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'U' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR U  32 " --> pdb=" O   LYS U  28 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS U  59 " --> pdb=" O   GLN U  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG U  60 " --> pdb=" O   PHE U  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR U  61 " --> pdb=" O   LYS U  58 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 74 through 91
      removed outlier: 3.994A  pdb=" N   THR U  78 " --> pdb=" O   THR U  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS U  79 " --> pdb=" O   ILE U  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER U  90 " --> pdb=" O   GLU U  86 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 97 through 102
    Processing helix  chain 'U' and resid 107 through 119
    Processing helix  chain 'U' and resid 128 through 141
      removed outlier: 3.696A  pdb=" N   LEU U 132 " --> pdb=" O   SER U 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU U 133 " --> pdb=" O   LYS U 129 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 148 through 152
    Processing helix  chain 'U' and resid 199 through 210
      removed outlier: 3.684A  pdb=" N   GLU U 208 " --> pdb=" O   GLU U 204 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA U 243 " --> pdb=" O   ASP U 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR U 244 " --> pdb=" O   ARG U 240 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 266 through 279
    Processing helix  chain 'U' and resid 281 through 286
    Processing helix  chain 'U' and resid 287 through 289
      No H-bonds generated for 'chain 'U' and resid 287 through 289'
    Processing helix  chain 'U' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER U 313 " --> pdb=" O   MET U 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS A  59 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A  60 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR A  61 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR A  78 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER A  90 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 102
    Processing helix  chain 'A' and resid 107 through 119
    Processing helix  chain 'A' and resid 128 through 141
      removed outlier: 3.695A  pdb=" N   LEU A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A 133 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA A 243 " --> pdb=" O   ASP A 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 279
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'A' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER A 313 " --> pdb=" O   MET A 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR B  32 " --> pdb=" O   LYS B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS B  59 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG B  60 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR B  61 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR B  78 " --> pdb=" O   THR B  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS B  79 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER B  90 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 107 through 119
    Processing helix  chain 'B' and resid 128 through 141
      removed outlier: 3.696A  pdb=" N   LEU B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 152
    Processing helix  chain 'B' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA B 243 " --> pdb=" O   ASP B 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 244 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 279
    Processing helix  chain 'B' and resid 281 through 286
    Processing helix  chain 'B' and resid 287 through 289
      No H-bonds generated for 'chain 'B' and resid 287 through 289'
    Processing helix  chain 'B' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER B 313 " --> pdb=" O   MET B 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR C  32 " --> pdb=" O   LYS C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS C  59 " --> pdb=" O   GLN C  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG C  60 " --> pdb=" O   PHE C  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR C  61 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS C  79 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER C  90 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 102
    Processing helix  chain 'C' and resid 107 through 119
    Processing helix  chain 'C' and resid 128 through 141
      removed outlier: 3.697A  pdb=" N   LEU C 132 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU C 133 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 152
    Processing helix  chain 'C' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU C 208 " --> pdb=" O   GLU C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA C 243 " --> pdb=" O   ASP C 239 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR C 244 " --> pdb=" O   ARG C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 279
    Processing helix  chain 'C' and resid 281 through 286
    Processing helix  chain 'C' and resid 287 through 289
      No H-bonds generated for 'chain 'C' and resid 287 through 289'
    Processing helix  chain 'C' and resid 303 through 313
      removed outlier: 3.753A  pdb=" N   SER C 313 " --> pdb=" O   MET C 309 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR D  32 " --> pdb=" O   LYS D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS D  59 " --> pdb=" O   GLN D  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG D  60 " --> pdb=" O   PHE D  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR D  61 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR D  78 " --> pdb=" O   THR D  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS D  79 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER D  90 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 102
    Processing helix  chain 'D' and resid 107 through 119
    Processing helix  chain 'D' and resid 128 through 141
      removed outlier: 3.696A  pdb=" N   LEU D 132 " --> pdb=" O   SER D 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU D 133 " --> pdb=" O   LYS D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 152
    Processing helix  chain 'D' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU D 208 " --> pdb=" O   GLU D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA D 243 " --> pdb=" O   ASP D 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR D 244 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 266 through 279
    Processing helix  chain 'D' and resid 281 through 286
    Processing helix  chain 'D' and resid 287 through 289
      No H-bonds generated for 'chain 'D' and resid 287 through 289'
    Processing helix  chain 'D' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER D 313 " --> pdb=" O   MET D 309 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR E  32 " --> pdb=" O   LYS E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS E  59 " --> pdb=" O   GLN E  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG E  60 " --> pdb=" O   PHE E  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR E  61 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR E  78 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS E  79 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER E  90 " --> pdb=" O   GLU E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 102
    Processing helix  chain 'E' and resid 107 through 119
    Processing helix  chain 'E' and resid 128 through 141
      removed outlier: 3.696A  pdb=" N   LEU E 132 " --> pdb=" O   SER E 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU E 133 " --> pdb=" O   LYS E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 152
    Processing helix  chain 'E' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU E 208 " --> pdb=" O   GLU E 204 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA E 243 " --> pdb=" O   ASP E 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR E 244 " --> pdb=" O   ARG E 240 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 279
    Processing helix  chain 'E' and resid 281 through 286
    Processing helix  chain 'E' and resid 287 through 289
      No H-bonds generated for 'chain 'E' and resid 287 through 289'
    Processing helix  chain 'E' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER E 313 " --> pdb=" O   MET E 309 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR F  32 " --> pdb=" O   LYS F  28 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS F  59 " --> pdb=" O   GLN F  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG F  60 " --> pdb=" O   PHE F  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR F  61 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR F  78 " --> pdb=" O   THR F  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS F  79 " --> pdb=" O   ILE F  75 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER F  90 " --> pdb=" O   GLU F  86 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 102
    Processing helix  chain 'F' and resid 107 through 119
    Processing helix  chain 'F' and resid 128 through 141
      removed outlier: 3.696A  pdb=" N   LEU F 132 " --> pdb=" O   SER F 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU F 133 " --> pdb=" O   LYS F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 148 through 152
    Processing helix  chain 'F' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU F 208 " --> pdb=" O   GLU F 204 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA F 243 " --> pdb=" O   ASP F 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR F 244 " --> pdb=" O   ARG F 240 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 266 through 279
    Processing helix  chain 'F' and resid 281 through 286
    Processing helix  chain 'F' and resid 287 through 289
      No H-bonds generated for 'chain 'F' and resid 287 through 289'
    Processing helix  chain 'F' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER F 313 " --> pdb=" O   MET F 309 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 23 through 32
      removed outlier: 3.855A  pdb=" N   THR G  32 " --> pdb=" O   LYS G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 54 through 61
      removed outlier: 4.865A  pdb=" N   LYS G  59 " --> pdb=" O   GLN G  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG G  60 " --> pdb=" O   PHE G  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR G  61 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 74 through 91
      removed outlier: 3.995A  pdb=" N   THR G  78 " --> pdb=" O   THR G  74 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS G  79 " --> pdb=" O   ILE G  75 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER G  90 " --> pdb=" O   GLU G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 97 through 102
    Processing helix  chain 'G' and resid 107 through 119
    Processing helix  chain 'G' and resid 128 through 141
      removed outlier: 3.696A  pdb=" N   LEU G 132 " --> pdb=" O   SER G 128 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU G 133 " --> pdb=" O   LYS G 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 148 through 152
    Processing helix  chain 'G' and resid 199 through 210
      removed outlier: 3.685A  pdb=" N   GLU G 208 " --> pdb=" O   GLU G 204 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 233 through 247
      removed outlier: 4.016A  pdb=" N   ALA G 243 " --> pdb=" O   ASP G 239 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR G 244 " --> pdb=" O   ARG G 240 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 266 through 279
    Processing helix  chain 'G' and resid 281 through 286
    Processing helix  chain 'G' and resid 287 through 289
      No H-bonds generated for 'chain 'G' and resid 287 through 289'
    Processing helix  chain 'G' and resid 303 through 313
      removed outlier: 3.752A  pdb=" N   SER G 313 " --> pdb=" O   MET G 309 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'U' and resid 8 through 12
    Processing sheet with id=AA2, first strand: chain 'U' and resid 44 through 46
    Processing sheet with id=AA3, first strand: chain 'U' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE U 157 " --> pdb=" O   LYS U 168 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LYS U 168 " --> pdb=" O   ILE U 157 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE U 159 " --> pdb=" O   MET U 166 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 8 through 12
    Processing sheet with id=AA5, first strand: chain 'A' and resid 44 through 46
    Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE A 157 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LYS A 168 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE A 159 " --> pdb=" O   MET A 166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12
    Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 46
    Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE B 157 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LYS B 168 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE B 159 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 12
    Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 46
    Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE C 157 " --> pdb=" O   LYS C 168 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LYS C 168 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE C 159 " --> pdb=" O   MET C 166 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 8 through 12
    Processing sheet with id=AB5, first strand: chain 'D' and resid 44 through 46
    Processing sheet with id=AB6, first strand: chain 'D' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE D 157 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LYS D 168 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE D 159 " --> pdb=" O   MET D 166 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 8 through 12
    Processing sheet with id=AB8, first strand: chain 'E' and resid 44 through 46
    Processing sheet with id=AB9, first strand: chain 'E' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE E 157 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LYS E 168 " --> pdb=" O   ILE E 157 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE E 159 " --> pdb=" O   MET E 166 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 8 through 12
    Processing sheet with id=AC2, first strand: chain 'F' and resid 44 through 46
    Processing sheet with id=AC3, first strand: chain 'F' and resid 157 through 160
      removed outlier: 6.189A  pdb=" N   ILE F 157 " --> pdb=" O   LYS F 168 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LYS F 168 " --> pdb=" O   ILE F 157 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE F 159 " --> pdb=" O   MET F 166 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 8 through 12
    Processing sheet with id=AC5, first strand: chain 'G' and resid 44 through 46
    Processing sheet with id=AC6, first strand: chain 'G' and resid 157 through 160
      removed outlier: 6.188A  pdb=" N   ILE G 157 " --> pdb=" O   LYS G 168 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LYS G 168 " --> pdb=" O   ILE G 157 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   PHE G 159 " --> pdb=" O   MET G 166 " (cutoff:3.500A)

    752 hydrogen bonds defined for protein.
    2112 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: 3.14

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6496
        1.34 -     1.45: 2980
        1.45 -     1.57: 11108
        1.57 -     1.69: 0
        1.69 -     1.80: 208
  Bond restraints: 20792
  Sorted by residual:
  bond pdb=" C   SER U  67 "
       pdb=" N   ARG U  68 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 1.24e-02 6.50e+03 1.10e+01
  bond pdb=" C   SER F  67 "
       pdb=" N   ARG F  68 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.041 1.24e-02 6.50e+03 1.08e+01
  bond pdb=" C   SER A  67 "
       pdb=" N   ARG A  68 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.041 1.24e-02 6.50e+03 1.08e+01
  bond pdb=" C   SER B  67 "
       pdb=" N   ARG B  68 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.041 1.24e-02 6.50e+03 1.08e+01
  bond pdb=" C   SER G  67 "
       pdb=" N   ARG G  68 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.041 1.24e-02 6.50e+03 1.08e+01
  ... (remaining 20787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 26695
        1.43 -     2.86: 1186
        2.86 -     4.29: 135
        4.29 -     5.72: 40
        5.72 -     7.15: 16
  Bond angle restraints: 28072
  Sorted by residual:
  angle pdb=" N   LYS D  38 "
        pdb=" CA  LYS D  38 "
        pdb=" C   LYS D  38 "
      ideal   model   delta    sigma   weight residual
     114.56  107.41    7.15 1.27e+00 6.20e-01 3.17e+01
  angle pdb=" N   LYS U  38 "
        pdb=" CA  LYS U  38 "
        pdb=" C   LYS U  38 "
      ideal   model   delta    sigma   weight residual
     114.56  107.41    7.15 1.27e+00 6.20e-01 3.17e+01
  angle pdb=" N   LYS E  38 "
        pdb=" CA  LYS E  38 "
        pdb=" C   LYS E  38 "
      ideal   model   delta    sigma   weight residual
     114.56  107.41    7.15 1.27e+00 6.20e-01 3.17e+01
  angle pdb=" N   LYS F  38 "
        pdb=" CA  LYS F  38 "
        pdb=" C   LYS F  38 "
      ideal   model   delta    sigma   weight residual
     114.56  107.41    7.15 1.27e+00 6.20e-01 3.17e+01
  angle pdb=" N   LYS B  38 "
        pdb=" CA  LYS B  38 "
        pdb=" C   LYS B  38 "
      ideal   model   delta    sigma   weight residual
     114.56  107.41    7.15 1.27e+00 6.20e-01 3.17e+01
  ... (remaining 28067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 11111
       16.07 -    32.14: 1184
       32.14 -    48.21: 289
       48.21 -    64.28: 31
       64.28 -    80.34: 25
  Dihedral angle restraints: 12640
    sinusoidal: 5200
      harmonic: 7440
  Sorted by residual:
  dihedral pdb=" CA  GLU G  13 "
           pdb=" C   GLU G  13 "
           pdb=" N   ASN G  14 "
           pdb=" CA  ASN G  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.73   16.27     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  GLU E  13 "
           pdb=" C   GLU E  13 "
           pdb=" N   ASN E  14 "
           pdb=" CA  ASN E  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  GLU F  13 "
           pdb=" C   GLU F  13 "
           pdb=" N   ASN F  14 "
           pdb=" CA  ASN F  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 12637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1356
       0.025 -    0.050: 1049
       0.050 -    0.074: 491
       0.074 -    0.099: 128
       0.099 -    0.124: 112
  Chirality restraints: 3136
  Sorted by residual:
  chirality pdb=" CA  ILE G 228 "
            pdb=" N   ILE G 228 "
            pdb=" C   ILE G 228 "
            pdb=" CB  ILE G 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE A 228 "
            pdb=" N   ILE A 228 "
            pdb=" C   ILE A 228 "
            pdb=" CB  ILE A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  chirality pdb=" CA  ILE F 228 "
            pdb=" N   ILE F 228 "
            pdb=" C   ILE F 228 "
            pdb=" CB  ILE F 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 3133 not shown)

  Planarity restraints: 3552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG U  68 "    0.011 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   ARG U  68 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG U  68 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY U  69 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG F  68 "    0.011 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   ARG F  68 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG F  68 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY F  69 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  68 "    0.011 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   ARG A  68 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG A  68 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY A  69 "    0.014 2.00e-02 2.50e+03
  ... (remaining 3549 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 4654
        2.77 -     3.30: 17831
        3.30 -     3.84: 30948
        3.84 -     4.37: 38945
        4.37 -     4.90: 67639
  Nonbonded interactions: 160017
  Sorted by model distance:
  nonbonded pdb=" CD2 PHE F 257 "
            pdb=" CD1 LEU F 259 "
     model   vdw
     2.238 3.760
  nonbonded pdb=" CD2 PHE A 257 "
            pdb=" CD1 LEU A 259 "
     model   vdw
     2.238 3.760
  nonbonded pdb=" CD2 PHE D 257 "
            pdb=" CD1 LEU D 259 "
     model   vdw
     2.238 3.760
  nonbonded pdb=" CD2 PHE B 257 "
            pdb=" CD1 LEU B 259 "
     model   vdw
     2.238 3.760
  nonbonded pdb=" CD2 PHE U 257 "
            pdb=" CD1 LEU U 259 "
     model   vdw
     2.238 3.760
  ... (remaining 160012 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'U'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     17.050
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
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      :  0.008   0.041  20792  Z= 0.333
  Angle     :  0.688   7.145  28072  Z= 0.411
  Chirality :  0.043   0.124   3136
  Planarity :  0.004   0.039   3552
  Dihedral  : 14.184  80.344   7792
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (0.14), residues: 2488
  helix: -1.85 (0.15), residues: 912
  sheet: -1.94 (0.27), residues: 264
  loop : -3.63 (0.13), residues: 1312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U 104 
 TYR   0.009   0.002   TYR D  44 
 PHE   0.017   0.002   PHE C  77 
 TRP   0.010   0.002   TRP D 167 
 HIS   0.003   0.001   HIS G 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00763 (20792)
  covalent geometry    : angle       0.68766 (28072)
  hydrogen bonds       : bond        0.20526 (  752)
  hydrogen bonds       : angle       6.93701 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 336
  time to evaluate  : 0.765 
Fit side-chains
REVERT: U   40 MET cc_start: 0.7977 (mmt) cc_final: 0.7759 (tpp)
REVERT: U  183 ASN cc_start: 0.7993 (m-40) cc_final: 0.7770 (p0)
REVERT: U  197 ILE cc_start: 0.8700 (mm) cc_final: 0.8308 (mm)
REVERT: U  240 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7686 (ttm-80)
REVERT: A   40 MET cc_start: 0.7975 (mmt) cc_final: 0.7754 (tpp)
REVERT: A  183 ASN cc_start: 0.7993 (m-40) cc_final: 0.7769 (p0)
REVERT: A  197 ILE cc_start: 0.8697 (mm) cc_final: 0.8306 (mm)
REVERT: A  240 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7687 (ttm-80)
REVERT: B   40 MET cc_start: 0.7973 (mmt) cc_final: 0.7753 (tpp)
REVERT: B  183 ASN cc_start: 0.7996 (m-40) cc_final: 0.7771 (p0)
REVERT: B  197 ILE cc_start: 0.8694 (mm) cc_final: 0.8304 (mm)
REVERT: B  240 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7686 (ttm-80)
REVERT: C   40 MET cc_start: 0.7974 (mmt) cc_final: 0.7753 (tpp)
REVERT: C  183 ASN cc_start: 0.7992 (m-40) cc_final: 0.7769 (p0)
REVERT: C  197 ILE cc_start: 0.8702 (mm) cc_final: 0.8311 (mm)
REVERT: C  240 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7682 (ttm-80)
REVERT: D   40 MET cc_start: 0.7975 (mmt) cc_final: 0.7755 (tpp)
REVERT: D  183 ASN cc_start: 0.7996 (m-40) cc_final: 0.7771 (p0)
REVERT: D  197 ILE cc_start: 0.8712 (mm) cc_final: 0.8321 (mm)
REVERT: D  240 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7686 (ttm-80)
REVERT: E   40 MET cc_start: 0.7975 (mmt) cc_final: 0.7757 (tpp)
REVERT: E  183 ASN cc_start: 0.7991 (m-40) cc_final: 0.7766 (p0)
REVERT: E  197 ILE cc_start: 0.8697 (mm) cc_final: 0.8307 (mm)
REVERT: E  240 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7687 (ttm-80)
REVERT: F   40 MET cc_start: 0.7977 (mmt) cc_final: 0.7758 (tpp)
REVERT: F  183 ASN cc_start: 0.7991 (m-40) cc_final: 0.7767 (p0)
REVERT: F  197 ILE cc_start: 0.8697 (mm) cc_final: 0.8306 (mm)
REVERT: F  240 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7688 (ttm-80)
REVERT: G   40 MET cc_start: 0.7974 (mmt) cc_final: 0.7753 (tpp)
REVERT: G  183 ASN cc_start: 0.7994 (m-40) cc_final: 0.7770 (p0)
REVERT: G  197 ILE cc_start: 0.8695 (mm) cc_final: 0.8306 (mm)
REVERT: G  240 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7688 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 336
  average time/residue: 0.1978
  time to fit residues: 93.5755
Evaluate side-chains
  264 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 216 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 194 optimal weight:    0.9990
   chunk 227 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 247 optimal weight:    8.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 110 HIS
U 127 HIS
U 175 GLN
** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 258 ASN
A  95 GLN
A 110 HIS
A 127 HIS
A 175 GLN
A 248 ASN
A 258 ASN
B  95 GLN
B 110 HIS
B 127 HIS
B 175 GLN
B 248 ASN
B 258 ASN
C  95 GLN
C 110 HIS
C 127 HIS
C 175 GLN
C 248 ASN
C 258 ASN
D  95 GLN
D 110 HIS
D 127 HIS
D 175 GLN
** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 258 ASN
E  95 GLN
E 110 HIS
E 127 HIS
E 175 GLN
E 248 ASN
E 258 ASN
F  95 GLN
F 110 HIS
F 127 HIS
F 175 GLN
** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 258 ASN
G  95 GLN
G 110 HIS
G 127 HIS
G 175 GLN
G 248 ASN
G 258 ASN

Total number of N/Q/H flips: 45

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.162120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119166 restraints weight = 23247.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 3.06
r_work: 0.2951 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026  20792  Z= 0.200
  Angle     :  0.555   6.412  28072  Z= 0.291
  Chirality :  0.043   0.134   3136
  Planarity :  0.004   0.030   3552
  Dihedral  :  4.541  16.086   2680
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.01 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.15), residues: 2488
  helix: -0.97 (0.16), residues: 1008
  sheet: -1.65 (0.27), residues: 264
  loop : -3.26 (0.14), residues: 1216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  60 
 TYR   0.007   0.001   TYR G 226 
 PHE   0.015   0.001   PHE C  77 
 TRP   0.006   0.002   TRP E 167 
 HIS   0.002   0.001   HIS D 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (20792)
  covalent geometry    : angle       0.55529 (28072)
  hydrogen bonds       : bond        0.04389 (  752)
  hydrogen bonds       : angle       4.98216 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 280
  time to evaluate  : 0.832 
Fit side-chains
REVERT: U   68 ARG cc_start: 0.7900 (ptt-90) cc_final: 0.7692 (mtm110)
REVERT: U  183 ASN cc_start: 0.8136 (m-40) cc_final: 0.7602 (p0)
REVERT: U  197 ILE cc_start: 0.8620 (mm) cc_final: 0.8194 (mm)
REVERT: U  227 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7786 (ttt90)
REVERT: U  240 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7707 (ttm170)
REVERT: A   68 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.7690 (mtm110)
REVERT: A  183 ASN cc_start: 0.8140 (m-40) cc_final: 0.7613 (p0)
REVERT: A  197 ILE cc_start: 0.8621 (mm) cc_final: 0.8196 (mm)
REVERT: A  227 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7791 (ttt90)
REVERT: A  240 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7710 (ttm170)
REVERT: B   68 ARG cc_start: 0.7892 (ptt-90) cc_final: 0.7685 (mtm110)
REVERT: B  183 ASN cc_start: 0.8128 (m-40) cc_final: 0.7595 (p0)
REVERT: B  197 ILE cc_start: 0.8625 (mm) cc_final: 0.8200 (mm)
REVERT: B  227 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7788 (ttt90)
REVERT: B  240 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7708 (ttm170)
REVERT: C   68 ARG cc_start: 0.7921 (ptt-90) cc_final: 0.7717 (mtm110)
REVERT: C  183 ASN cc_start: 0.8115 (m-40) cc_final: 0.7579 (p0)
REVERT: C  197 ILE cc_start: 0.8619 (mm) cc_final: 0.8196 (mm)
REVERT: C  227 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7776 (ttt90)
REVERT: C  240 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7717 (ttm170)
REVERT: D   68 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7694 (mtm110)
REVERT: D  183 ASN cc_start: 0.8125 (m-40) cc_final: 0.7588 (p0)
REVERT: D  197 ILE cc_start: 0.8627 (mm) cc_final: 0.8205 (mm)
REVERT: D  227 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7779 (ttt90)
REVERT: D  240 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7698 (ttm170)
REVERT: E   68 ARG cc_start: 0.7895 (ptt-90) cc_final: 0.7687 (mtm110)
REVERT: E  183 ASN cc_start: 0.8138 (m-40) cc_final: 0.7602 (p0)
REVERT: E  197 ILE cc_start: 0.8626 (mm) cc_final: 0.8199 (mm)
REVERT: E  227 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7787 (ttt90)
REVERT: E  240 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7702 (ttm170)
REVERT: F   68 ARG cc_start: 0.7904 (ptt-90) cc_final: 0.7700 (mtm110)
REVERT: F  183 ASN cc_start: 0.8132 (m-40) cc_final: 0.7600 (p0)
REVERT: F  197 ILE cc_start: 0.8629 (mm) cc_final: 0.8204 (mm)
REVERT: F  227 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7788 (ttt90)
REVERT: F  240 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7730 (ttm170)
REVERT: G   68 ARG cc_start: 0.7890 (ptt-90) cc_final: 0.7686 (mtm110)
REVERT: G  183 ASN cc_start: 0.8119 (m-40) cc_final: 0.7575 (p0)
REVERT: G  197 ILE cc_start: 0.8622 (mm) cc_final: 0.8199 (mm)
REVERT: G  227 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7772 (ttt90)
REVERT: G  240 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7733 (ttm170)
  outliers start: 40
  outliers final: 32
  residues processed: 304
  average time/residue: 0.1812
  time to fit residues: 79.4401
Evaluate side-chains
  288 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 256
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain U residue  310 ASP
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  310 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  305 THR
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 183 optimal weight:    6.9990
   chunk 169 optimal weight:    9.9990
   chunk 225 optimal weight:    0.9990
   chunk 135 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 141 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   chunk 130 optimal weight:    0.0770
   chunk 90 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    1.6146

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 127 HIS
** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 255 ASN
A  95 GLN
A 127 HIS
A 255 ASN
B  95 GLN
B 127 HIS
B 255 ASN
C  95 GLN
C 127 HIS
C 255 ASN
D  95 GLN
D 127 HIS
** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN
E  95 GLN
E 127 HIS
E 255 ASN
F  95 GLN
F 127 HIS
** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 255 ASN
G  95 GLN
G 127 HIS
G 255 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.162750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.114873 restraints weight = 23361.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 3.84
r_work: 0.2937 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  20792  Z= 0.134
  Angle     :  0.472   6.025  28072  Z= 0.251
  Chirality :  0.040   0.127   3136
  Planarity :  0.003   0.030   3552
  Dihedral  :  4.110  14.637   2680
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.15 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.15), residues: 2488
  helix: -0.07 (0.17), residues: 1008
  sheet: -1.25 (0.27), residues: 264
  loop : -2.92 (0.14), residues: 1216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  60 
 TYR   0.006   0.001   TYR U 226 
 PHE   0.010   0.001   PHE U  77 
 TRP   0.006   0.001   TRP D 167 
 HIS   0.003   0.001   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (20792)
  covalent geometry    : angle       0.47159 (28072)
  hydrogen bonds       : bond        0.03561 (  752)
  hydrogen bonds       : angle       4.48724 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 305
  time to evaluate  : 0.845 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8189 (m-40) cc_final: 0.7629 (p0)
REVERT: U  197 ILE cc_start: 0.8639 (mm) cc_final: 0.8177 (mm)
REVERT: U  227 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7742 (ttt90)
REVERT: U  240 ARG cc_start: 0.8142 (ttm170) cc_final: 0.7872 (ttm170)
REVERT: U  255 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7307 (p0)
REVERT: A  183 ASN cc_start: 0.8188 (m-40) cc_final: 0.7636 (p0)
REVERT: A  197 ILE cc_start: 0.8638 (mm) cc_final: 0.8178 (mm)
REVERT: A  227 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7716 (ttt90)
REVERT: A  240 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7874 (ttm170)
REVERT: A  255 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7340 (p0)
REVERT: B  183 ASN cc_start: 0.8192 (m-40) cc_final: 0.7637 (p0)
REVERT: B  197 ILE cc_start: 0.8634 (mm) cc_final: 0.8174 (mm)
REVERT: B  227 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7716 (ttt90)
REVERT: B  240 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7859 (ttm170)
REVERT: B  255 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7348 (p0)
REVERT: C  119 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7803 (mt-10)
REVERT: C  183 ASN cc_start: 0.8199 (m-40) cc_final: 0.7647 (p0)
REVERT: C  197 ILE cc_start: 0.8638 (mm) cc_final: 0.8175 (mm)
REVERT: C  227 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7727 (ttt90)
REVERT: C  240 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7853 (ttm170)
REVERT: C  255 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7342 (p0)
REVERT: D  183 ASN cc_start: 0.8192 (m-40) cc_final: 0.7631 (p0)
REVERT: D  197 ILE cc_start: 0.8638 (mm) cc_final: 0.8176 (mm)
REVERT: D  227 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7722 (ttt90)
REVERT: D  240 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7839 (ttm170)
REVERT: D  255 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7290 (p0)
REVERT: E  183 ASN cc_start: 0.8193 (m-40) cc_final: 0.7633 (p0)
REVERT: E  197 ILE cc_start: 0.8637 (mm) cc_final: 0.8176 (mm)
REVERT: E  227 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7725 (ttt90)
REVERT: E  240 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7855 (ttm170)
REVERT: E  255 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7320 (p0)
REVERT: F  183 ASN cc_start: 0.8184 (m-40) cc_final: 0.7633 (p0)
REVERT: F  197 ILE cc_start: 0.8634 (mm) cc_final: 0.8174 (mm)
REVERT: F  227 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7717 (ttt90)
REVERT: F  240 ARG cc_start: 0.8116 (ttm170) cc_final: 0.7843 (ttm170)
REVERT: F  255 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7282 (p0)
REVERT: G  183 ASN cc_start: 0.8195 (m-40) cc_final: 0.7637 (p0)
REVERT: G  197 ILE cc_start: 0.8625 (mm) cc_final: 0.8164 (mm)
REVERT: G  227 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7724 (ttt90)
REVERT: G  240 ARG cc_start: 0.8132 (ttm170) cc_final: 0.7861 (ttm170)
REVERT: G  255 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7340 (p0)
  outliers start: 44
  outliers final: 35
  residues processed: 330
  average time/residue: 0.1746
  time to fit residues: 83.9521
Evaluate side-chains
  324 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 280
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  255 ASN
Chi-restraints excluded: chain U residue  310 ASP
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  255 ASN
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  255 ASN
Chi-restraints excluded: chain D residue  310 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  255 ASN
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  255 ASN
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 86 optimal weight:    7.9990
   chunk 184 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 124 optimal weight:    8.9990
   chunk 183 optimal weight:    7.9990
   chunk 188 optimal weight:    5.9990
   chunk 227 optimal weight:    6.9990
   chunk 243 optimal weight:    6.9990
   chunk 106 optimal weight:    0.8980
   chunk 240 optimal weight:    2.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
U  62 ASN
U  95 GLN
** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 255 ASN
A  62 ASN
A  95 GLN
A 255 ASN
B  62 ASN
B  95 GLN
B 255 ASN
C  62 ASN
C  95 GLN
C 255 ASN
D  62 ASN
D  95 GLN
** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN
E  62 ASN
E  95 GLN
E 255 ASN
F  62 ASN
F  95 GLN
** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 255 ASN
G  62 ASN
G  95 GLN
G 255 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.167271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.123125 restraints weight = 23398.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 3.27
r_work: 0.2950 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  20792  Z= 0.263
  Angle     :  0.565   5.773  28072  Z= 0.292
  Chirality :  0.044   0.120   3136
  Planarity :  0.004   0.036   3552
  Dihedral  :  4.451  15.733   2680
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.36 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.15), residues: 2488
  helix: -0.32 (0.16), residues: 1056
  sheet: -1.15 (0.28), residues: 264
  loop : -2.91 (0.15), residues: 1168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  60 
 TYR   0.008   0.002   TYR U 226 
 PHE   0.019   0.002   PHE D  77 
 TRP   0.010   0.002   TRP D 167 
 HIS   0.002   0.001   HIS C 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 (20792)
  covalent geometry    : angle       0.56494 (28072)
  hydrogen bonds       : bond        0.04633 (  752)
  hydrogen bonds       : angle       4.73482 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 264
  time to evaluate  : 0.786 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8147 (m-40) cc_final: 0.7664 (p0)
REVERT: U  227 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7828 (ttt90)
REVERT: U  240 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7856 (ttm170)
REVERT: U  255 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7490 (p0)
REVERT: A  183 ASN cc_start: 0.8138 (m-40) cc_final: 0.7664 (p0)
REVERT: A  227 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7758 (ttt90)
REVERT: A  240 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7853 (ttm170)
REVERT: A  255 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7526 (p0)
REVERT: B  183 ASN cc_start: 0.8152 (m-40) cc_final: 0.7662 (p0)
REVERT: B  227 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7763 (ttt90)
REVERT: B  240 ARG cc_start: 0.8130 (ttm170) cc_final: 0.7857 (ttm170)
REVERT: B  255 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7545 (p0)
REVERT: C  183 ASN cc_start: 0.8146 (m-40) cc_final: 0.7670 (p0)
REVERT: C  227 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7766 (ttt90)
REVERT: C  240 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7865 (ttm170)
REVERT: C  255 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7532 (p0)
REVERT: D  183 ASN cc_start: 0.8148 (m-40) cc_final: 0.7662 (p0)
REVERT: D  227 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7763 (ttt90)
REVERT: D  240 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7855 (ttm170)
REVERT: D  255 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7487 (p0)
REVERT: E  183 ASN cc_start: 0.8145 (m-40) cc_final: 0.7664 (p0)
REVERT: E  227 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7763 (ttt90)
REVERT: E  240 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7832 (ttm170)
REVERT: E  255 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7520 (p0)
REVERT: F  183 ASN cc_start: 0.8149 (m-40) cc_final: 0.7666 (p0)
REVERT: F  227 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7750 (ttt90)
REVERT: F  240 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7853 (ttm170)
REVERT: F  255 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7468 (p0)
REVERT: G  183 ASN cc_start: 0.8157 (m-40) cc_final: 0.7677 (p0)
REVERT: G  227 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7813 (ttt90)
REVERT: G  240 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7879 (ttm170)
REVERT: G  255 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7534 (p0)
  outliers start: 80
  outliers final: 56
  residues processed: 304
  average time/residue: 0.1763
  time to fit residues: 77.0665
Evaluate side-chains
  320 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 256
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  255 ASN
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain U residue  310 ASP
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  255 ASN
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  255 ASN
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  310 ASP
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   78 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  255 ASN
Chi-restraints excluded: chain F residue  305 THR
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   78 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  255 ASN
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0060
   chunk 229 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 136 optimal weight:    0.8980
   chunk 159 optimal weight:    2.9990
   chunk 176 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 239 optimal weight:    0.7980
   chunk 133 optimal weight:    6.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 127 HIS
** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 255 ASN
A  95 GLN
A 127 HIS
A 255 ASN
B  95 GLN
B 127 HIS
B 255 ASN
C  95 GLN
C 127 HIS
C 255 ASN
D  95 GLN
D 127 HIS
** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN
E  95 GLN
E 127 HIS
E 255 ASN
F  95 GLN
F 127 HIS
F 248 ASN
F 255 ASN
G  95 GLN
G 127 HIS
G 255 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.165633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.121219 restraints weight = 23427.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 3.27
r_work: 0.3008 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  20792  Z= 0.088
  Angle     :  0.427   5.604  28072  Z= 0.231
  Chirality :  0.039   0.127   3136
  Planarity :  0.003   0.027   3552
  Dihedral  :  3.842  13.053   2680
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.51 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.16), residues: 2488
  helix:  0.60 (0.17), residues: 1008
  sheet: -1.22 (0.27), residues: 280
  loop : -2.53 (0.15), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG U  60 
 TYR   0.005   0.001   TYR G 226 
 PHE   0.006   0.001   PHE U  19 
 TRP   0.006   0.001   TRP B 167 
 HIS   0.004   0.001   HIS U 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 (20792)
  covalent geometry    : angle       0.42698 (28072)
  hydrogen bonds       : bond        0.02869 (  752)
  hydrogen bonds       : angle       4.19073 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 302
  time to evaluate  : 0.746 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8139 (m-40) cc_final: 0.7663 (p0)
REVERT: U  197 ILE cc_start: 0.8528 (mm) cc_final: 0.8073 (mm)
REVERT: U  227 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7697 (ttt90)
REVERT: U  240 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7753 (ttm170)
REVERT: A  183 ASN cc_start: 0.8141 (m-40) cc_final: 0.7662 (p0)
REVERT: A  197 ILE cc_start: 0.8531 (mm) cc_final: 0.8079 (mm)
REVERT: A  227 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7700 (ttt90)
REVERT: A  240 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7762 (ttm170)
REVERT: B  183 ASN cc_start: 0.8140 (m-40) cc_final: 0.7659 (p0)
REVERT: B  197 ILE cc_start: 0.8534 (mm) cc_final: 0.8078 (mm)
REVERT: B  227 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7697 (ttt90)
REVERT: B  240 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7755 (ttm170)
REVERT: C  119 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7594 (mt-10)
REVERT: C  183 ASN cc_start: 0.8157 (m-40) cc_final: 0.7692 (p0)
REVERT: C  197 ILE cc_start: 0.8535 (mm) cc_final: 0.8077 (mm)
REVERT: C  227 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7704 (ttt90)
REVERT: C  240 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7731 (ttm170)
REVERT: D  183 ASN cc_start: 0.8143 (m-40) cc_final: 0.7663 (p0)
REVERT: D  197 ILE cc_start: 0.8531 (mm) cc_final: 0.8075 (mm)
REVERT: D  227 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7701 (ttt90)
REVERT: D  240 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7735 (ttm170)
REVERT: E  183 ASN cc_start: 0.8140 (m-40) cc_final: 0.7670 (p0)
REVERT: E  197 ILE cc_start: 0.8534 (mm) cc_final: 0.8079 (mm)
REVERT: E  227 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7705 (ttt90)
REVERT: E  240 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7735 (ttm170)
REVERT: F  183 ASN cc_start: 0.8149 (m-40) cc_final: 0.7676 (p0)
REVERT: F  197 ILE cc_start: 0.8522 (mm) cc_final: 0.8071 (mm)
REVERT: F  227 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7697 (ttt90)
REVERT: F  240 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7732 (ttm170)
REVERT: G  183 ASN cc_start: 0.8156 (m-40) cc_final: 0.7675 (p0)
REVERT: G  197 ILE cc_start: 0.8521 (mm) cc_final: 0.8068 (mm)
REVERT: G  227 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7682 (ttt90)
REVERT: G  240 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7754 (ttm170)
  outliers start: 63
  outliers final: 48
  residues processed: 335
  average time/residue: 0.1762
  time to fit residues: 84.7792
Evaluate side-chains
  327 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 278
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   74 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  173 GLU
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  173 GLU
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  173 GLU
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 GLU
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  173 GLU
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  173 GLU
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 60 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9990
   chunk 221 optimal weight:    5.9990
   chunk 233 optimal weight:    3.9990
   chunk 237 optimal weight:    5.9990
   chunk 228 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 236 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 127 HIS
** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 255 ASN
A  95 GLN
A 127 HIS
A 255 ASN
B  95 GLN
B 127 HIS
B 255 ASN
C  95 GLN
C 127 HIS
C 255 ASN
D  95 GLN
D 127 HIS
** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN
E  95 GLN
E 127 HIS
E 255 ASN
F  95 GLN
F 127 HIS
F 255 ASN
G  95 GLN
G 127 HIS
G 255 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.168011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124318 restraints weight = 23181.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.32
r_work: 0.2953 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029  20792  Z= 0.211
  Angle     :  0.525   5.370  28072  Z= 0.272
  Chirality :  0.042   0.119   3136
  Planarity :  0.003   0.033   3552
  Dihedral  :  4.206  15.326   2680
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.33 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.16), residues: 2488
  helix:  0.15 (0.16), residues: 1056
  sheet: -0.76 (0.28), residues: 264
  loop : -2.62 (0.15), residues: 1168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  60 
 TYR   0.008   0.001   TYR E 226 
 PHE   0.017   0.002   PHE G  77 
 TRP   0.009   0.002   TRP A 167 
 HIS   0.002   0.001   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (20792)
  covalent geometry    : angle       0.52487 (28072)
  hydrogen bonds       : bond        0.04118 (  752)
  hydrogen bonds       : angle       4.47601 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 288
  time to evaluate  : 0.660 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8171 (m-40) cc_final: 0.7611 (p0)
REVERT: U  227 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7726 (ttt90)
REVERT: U  240 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7609 (ttm-80)
REVERT: U  255 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7319 (p0)
REVERT: A  183 ASN cc_start: 0.8168 (m-40) cc_final: 0.7624 (p0)
REVERT: A  227 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7722 (ttt90)
REVERT: A  240 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7596 (ttm-80)
REVERT: A  255 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7401 (p0)
REVERT: B  183 ASN cc_start: 0.8172 (m-40) cc_final: 0.7609 (p0)
REVERT: B  227 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7726 (ttt90)
REVERT: B  240 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7609 (ttm-80)
REVERT: B  255 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (p0)
REVERT: C  183 ASN cc_start: 0.8161 (m-40) cc_final: 0.7602 (p0)
REVERT: C  227 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7737 (ttt90)
REVERT: C  240 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7781 (ttm170)
REVERT: C  255 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7403 (p0)
REVERT: D  183 ASN cc_start: 0.8174 (m-40) cc_final: 0.7610 (p0)
REVERT: D  227 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7724 (ttt90)
REVERT: D  240 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7606 (ttm-80)
REVERT: D  255 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7336 (p0)
REVERT: E  183 ASN cc_start: 0.8166 (m-40) cc_final: 0.7608 (p0)
REVERT: E  227 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7729 (ttt90)
REVERT: E  240 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7573 (ttm-80)
REVERT: E  255 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7392 (p0)
REVERT: F  183 ASN cc_start: 0.8175 (m-40) cc_final: 0.7616 (p0)
REVERT: F  227 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7722 (ttt90)
REVERT: F  240 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7595 (ttm-80)
REVERT: F  255 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7341 (p0)
REVERT: G  183 ASN cc_start: 0.8189 (m-40) cc_final: 0.7630 (p0)
REVERT: G  227 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7690 (ttt90)
REVERT: G  240 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7611 (ttm-80)
REVERT: G  255 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7415 (p0)
  outliers start: 86
  outliers final: 78
  residues processed: 336
  average time/residue: 0.1730
  time to fit residues: 84.5338
Evaluate side-chains
  369 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 283
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   20 ILE
Chi-restraints excluded: chain U residue   74 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue   98 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  173 GLU
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  255 ASN
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain U residue  310 ASP
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  173 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  255 ASN
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   20 ILE
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  173 GLU
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  255 ASN
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  310 ASP
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   98 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 GLU
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue   98 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  173 GLU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  255 ASN
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue   98 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  173 GLU
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  255 ASN
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 173 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 157 optimal weight:    0.8980
   chunk 231 optimal weight:   10.0000
   chunk 144 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 216 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 127 HIS
U 248 ASN
U 255 ASN
A  95 GLN
A 127 HIS
A 255 ASN
B 127 HIS
B 255 ASN
C  95 GLN
C 127 HIS
C 255 ASN
D  95 GLN
D 127 HIS
D 248 ASN
D 255 ASN
E  95 GLN
E 127 HIS
E 255 ASN
F  95 GLN
F 127 HIS
F 255 ASN
G  95 GLN
G 127 HIS
G 255 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.165393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.120969 restraints weight = 23205.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 3.33
r_work: 0.3007 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  20792  Z= 0.093
  Angle     :  0.435   5.398  28072  Z= 0.234
  Chirality :  0.039   0.125   3136
  Planarity :  0.003   0.028   3552
  Dihedral  :  3.858  13.566   2680
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.55 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.16), residues: 2488
  helix:  0.58 (0.17), residues: 1056
  sheet: -1.08 (0.27), residues: 280
  loop : -2.43 (0.16), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  60 
 TYR   0.006   0.001   TYR B 226 
 PHE   0.006   0.001   PHE C  77 
 TRP   0.007   0.001   TRP E 167 
 HIS   0.003   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (20792)
  covalent geometry    : angle       0.43546 (28072)
  hydrogen bonds       : bond        0.03016 (  752)
  hydrogen bonds       : angle       4.16107 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 293
  time to evaluate  : 0.698 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8150 (m-40) cc_final: 0.7597 (p0)
REVERT: U  227 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7606 (ttt90)
REVERT: U  240 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7474 (ttm-80)
REVERT: U  255 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.7080 (p0)
REVERT: A  183 ASN cc_start: 0.8117 (m-40) cc_final: 0.7576 (p0)
REVERT: A  227 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7641 (ttt90)
REVERT: A  240 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7474 (ttm-80)
REVERT: A  255 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7201 (p0)
REVERT: B  183 ASN cc_start: 0.8135 (m-40) cc_final: 0.7578 (p0)
REVERT: B  227 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7632 (ttt90)
REVERT: B  240 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7472 (ttm-80)
REVERT: C  183 ASN cc_start: 0.8152 (m-40) cc_final: 0.7589 (p0)
REVERT: C  227 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7637 (ttt90)
REVERT: C  240 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7507 (ttm-80)
REVERT: C  255 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.7188 (p0)
REVERT: D  183 ASN cc_start: 0.8142 (m-40) cc_final: 0.7587 (p0)
REVERT: D  227 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7632 (ttt90)
REVERT: D  240 ARG cc_start: 0.7840 (ttm170) cc_final: 0.7467 (ttm-80)
REVERT: E  183 ASN cc_start: 0.8142 (m-40) cc_final: 0.7588 (p0)
REVERT: E  227 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7635 (ttt90)
REVERT: E  240 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7456 (ttm-80)
REVERT: E  255 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7195 (p0)
REVERT: F  183 ASN cc_start: 0.8148 (m-40) cc_final: 0.7588 (p0)
REVERT: F  227 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7640 (ttt90)
REVERT: F  240 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7463 (ttm-80)
REVERT: F  255 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7238 (p0)
REVERT: G  183 ASN cc_start: 0.8161 (m-40) cc_final: 0.7605 (p0)
REVERT: G  240 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7477 (ttm-80)
  outliers start: 86
  outliers final: 72
  residues processed: 341
  average time/residue: 0.1752
  time to fit residues: 87.4828
Evaluate side-chains
  368 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 291
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   74 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue   98 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  173 GLU
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  255 ASN
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain U residue  310 ASP
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  173 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  255 ASN
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  173 GLU
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  310 ASP
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   98 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 GLU
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  255 ASN
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue   98 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  173 GLU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  255 ASN
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue   98 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  173 GLU
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 170 optimal weight:    4.9990
   chunk 206 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 112 optimal weight:    1.9990
   chunk 157 optimal weight:    4.9990
   chunk 203 optimal weight:    1.9990
   chunk 204 optimal weight:    0.5980
   chunk 162 optimal weight:    0.4980
   chunk 225 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 255 ASN
A  95 GLN
B  95 GLN
B 255 ASN
C  95 GLN
C 255 ASN
D  95 GLN
D 255 ASN
E  95 GLN
F  95 GLN
F 255 ASN
G  95 GLN
G 255 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.168387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123823 restraints weight = 23148.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.27
r_work: 0.2995 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  20792  Z= 0.108
  Angle     :  0.444   5.352  28072  Z= 0.233
  Chirality :  0.039   0.123   3136
  Planarity :  0.003   0.029   3552
  Dihedral  :  3.800  13.269   2680
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.89 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.16), residues: 2488
  helix:  0.75 (0.17), residues: 1056
  sheet: -1.05 (0.27), residues: 280
  loop : -2.36 (0.16), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG U  60 
 TYR   0.006   0.001   TYR G 226 
 PHE   0.008   0.001   PHE C  77 
 TRP   0.006   0.001   TRP F 167 
 HIS   0.004   0.001   HIS F 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (20792)
  covalent geometry    : angle       0.44382 (28072)
  hydrogen bonds       : bond        0.03112 (  752)
  hydrogen bonds       : angle       4.10454 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 290
  time to evaluate  : 0.639 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8143 (m-40) cc_final: 0.7615 (p0)
REVERT: U  240 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7461 (ttm-80)
REVERT: U  256 ASP cc_start: 0.7773 (t70) cc_final: 0.7529 (t70)
REVERT: A  183 ASN cc_start: 0.8142 (m-40) cc_final: 0.7616 (p0)
REVERT: A  240 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7447 (ttm-80)
REVERT: A  256 ASP cc_start: 0.7771 (t70) cc_final: 0.7531 (t70)
REVERT: B  183 ASN cc_start: 0.8130 (m-40) cc_final: 0.7606 (p0)
REVERT: B  240 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7444 (ttm-80)
REVERT: C  183 ASN cc_start: 0.8164 (m-40) cc_final: 0.7621 (p0)
REVERT: C  240 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7518 (ttm-80)
REVERT: C  256 ASP cc_start: 0.7783 (t70) cc_final: 0.7541 (t70)
REVERT: D  183 ASN cc_start: 0.8137 (m-40) cc_final: 0.7608 (p0)
REVERT: D  240 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7456 (ttm-80)
REVERT: E  183 ASN cc_start: 0.8136 (m-40) cc_final: 0.7608 (p0)
REVERT: E  240 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7431 (ttm-80)
REVERT: E  256 ASP cc_start: 0.7770 (t70) cc_final: 0.7529 (t70)
REVERT: F  183 ASN cc_start: 0.8143 (m-40) cc_final: 0.7609 (p0)
REVERT: F  240 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7453 (ttm-80)
REVERT: F  256 ASP cc_start: 0.7777 (t70) cc_final: 0.7537 (t70)
REVERT: G  183 ASN cc_start: 0.8151 (m-40) cc_final: 0.7620 (p0)
REVERT: G  240 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7436 (ttm-80)
  outliers start: 88
  outliers final: 72
  residues processed: 348
  average time/residue: 0.1569
  time to fit residues: 80.9328
Evaluate side-chains
  352 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 280
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   74 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue   98 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  173 GLU
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain U residue  310 ASP
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  173 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  173 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   20 ILE
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  173 GLU
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  310 ASP
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   98 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 GLU
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue   98 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  173 GLU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue   98 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  173 GLU
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 178 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 203 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0470
   chunk 45 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 168 optimal weight:    4.9990
   chunk 216 optimal weight:    6.9990
   chunk 213 optimal weight:    2.9990
   chunk 188 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7680

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
U 255 ASN
A  95 GLN
A 255 ASN
B  95 GLN
C  95 GLN
C 255 ASN
D  95 GLN
E  95 GLN
E 255 ASN
F  95 GLN
F 255 ASN
G  95 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.171731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.129027 restraints weight = 22834.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.08
r_work: 0.3024 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20792  Z= 0.085
  Angle     :  0.419   5.422  28072  Z= 0.222
  Chirality :  0.038   0.125   3136
  Planarity :  0.003   0.028   3552
  Dihedral  :  3.552  12.045   2680
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.08 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.17), residues: 2488
  helix:  1.40 (0.17), residues: 1008
  sheet: -0.92 (0.27), residues: 280
  loop : -2.11 (0.16), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  60 
 TYR   0.005   0.001   TYR D 226 
 PHE   0.006   0.001   PHE C  19 
 TRP   0.006   0.001   TRP E 167 
 HIS   0.003   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 (20792)
  covalent geometry    : angle       0.41937 (28072)
  hydrogen bonds       : bond        0.02691 (  752)
  hydrogen bonds       : angle       3.89494 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 273
  time to evaluate  : 0.772 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8122 (m-40) cc_final: 0.7617 (p0)
REVERT: U  197 ILE cc_start: 0.8543 (mm) cc_final: 0.8159 (mm)
REVERT: U  240 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7374 (ttm-80)
REVERT: A  183 ASN cc_start: 0.8131 (m-40) cc_final: 0.7618 (p0)
REVERT: A  197 ILE cc_start: 0.8538 (mm) cc_final: 0.8153 (mm)
REVERT: A  240 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7388 (ttm-80)
REVERT: B  183 ASN cc_start: 0.8108 (m-40) cc_final: 0.7600 (p0)
REVERT: B  197 ILE cc_start: 0.8540 (mm) cc_final: 0.8158 (mm)
REVERT: B  240 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7384 (ttm-80)
REVERT: B  256 ASP cc_start: 0.7733 (t70) cc_final: 0.7504 (t70)
REVERT: C  183 ASN cc_start: 0.8147 (m-40) cc_final: 0.7615 (p0)
REVERT: C  240 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7407 (ttm-80)
REVERT: D  183 ASN cc_start: 0.8113 (m-40) cc_final: 0.7603 (p0)
REVERT: D  197 ILE cc_start: 0.8547 (mm) cc_final: 0.8159 (mm)
REVERT: D  240 ARG cc_start: 0.7727 (ttm170) cc_final: 0.7375 (ttm-80)
REVERT: E  183 ASN cc_start: 0.8118 (m-40) cc_final: 0.7611 (p0)
REVERT: E  197 ILE cc_start: 0.8544 (mm) cc_final: 0.8161 (mm)
REVERT: E  240 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7360 (ttm-80)
REVERT: F  183 ASN cc_start: 0.8126 (m-40) cc_final: 0.7620 (p0)
REVERT: F  197 ILE cc_start: 0.8548 (mm) cc_final: 0.8162 (mm)
REVERT: F  240 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7359 (ttm-80)
REVERT: F  256 ASP cc_start: 0.7697 (t70) cc_final: 0.7460 (t70)
REVERT: G  183 ASN cc_start: 0.8133 (m-40) cc_final: 0.7620 (p0)
REVERT: G  197 ILE cc_start: 0.8541 (mm) cc_final: 0.8155 (mm)
REVERT: G  240 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7371 (ttm-80)
REVERT: G  256 ASP cc_start: 0.7751 (t70) cc_final: 0.7525 (t70)
  outliers start: 71
  outliers final: 65
  residues processed: 323
  average time/residue: 0.1635
  time to fit residues: 78.1621
Evaluate side-chains
  326 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 261
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   20 ILE
Chi-restraints excluded: chain U residue   74 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  173 GLU
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  173 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  173 GLU
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 GLU
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue   98 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  173 GLU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  173 GLU
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 130 optimal weight:    0.7980
   chunk 101 optimal weight:    0.8980
   chunk 149 optimal weight:    5.9990
   chunk 215 optimal weight:    6.9990
   chunk 156 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 151 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
U  95 GLN
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN
E  95 GLN
F  95 GLN
G  95 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.173072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.128391 restraints weight = 23220.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 3.19
r_work: 0.3060 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20792  Z= 0.098
  Angle     :  0.421   5.339  28072  Z= 0.223
  Chirality :  0.039   0.123   3136
  Planarity :  0.003   0.028   3552
  Dihedral  :  3.583  12.184   2680
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.99 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.17), residues: 2488
  helix:  1.49 (0.17), residues: 1008
  sheet: -0.79 (0.27), residues: 280
  loop : -2.06 (0.16), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG U  60 
 TYR   0.006   0.001   TYR U 226 
 PHE   0.008   0.001   PHE G  77 
 TRP   0.006   0.001   TRP U 167 
 HIS   0.004   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (20792)
  covalent geometry    : angle       0.42105 (28072)
  hydrogen bonds       : bond        0.02917 (  752)
  hydrogen bonds       : angle       3.90316 ( 2112)

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

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

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4976 Ramachandran restraints generated.
    2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 274
  time to evaluate  : 0.674 
Fit side-chains
REVERT: U  183 ASN cc_start: 0.8122 (m-40) cc_final: 0.7647 (p0)
REVERT: U  240 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7360 (ttm-80)
REVERT: A  183 ASN cc_start: 0.8129 (m-40) cc_final: 0.7649 (p0)
REVERT: A  240 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7372 (ttm-80)
REVERT: B  183 ASN cc_start: 0.8112 (m-40) cc_final: 0.7638 (p0)
REVERT: B  240 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7369 (ttm-80)
REVERT: B  256 ASP cc_start: 0.7840 (t70) cc_final: 0.7626 (t70)
REVERT: C  183 ASN cc_start: 0.8163 (m-40) cc_final: 0.7641 (p0)
REVERT: C  240 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7372 (ttm-80)
REVERT: D  183 ASN cc_start: 0.8128 (m-40) cc_final: 0.7638 (p0)
REVERT: D  240 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7367 (ttm-80)
REVERT: D  256 ASP cc_start: 0.7831 (t70) cc_final: 0.7622 (t70)
REVERT: E  183 ASN cc_start: 0.8121 (m-40) cc_final: 0.7648 (p0)
REVERT: E  240 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7348 (ttm-80)
REVERT: F  183 ASN cc_start: 0.8120 (m-40) cc_final: 0.7646 (p0)
REVERT: F  240 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7336 (ttm-80)
REVERT: G  183 ASN cc_start: 0.8127 (m-40) cc_final: 0.7640 (p0)
REVERT: G  240 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7355 (ttm-80)
REVERT: G  256 ASP cc_start: 0.7841 (t70) cc_final: 0.7628 (t70)
  outliers start: 72
  outliers final: 72
  residues processed: 326
  average time/residue: 0.1613
  time to fit residues: 77.9843
Evaluate side-chains
  343 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 271
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   20 ILE
Chi-restraints excluded: chain U residue   74 THR
Chi-restraints excluded: chain U residue   91 LEU
Chi-restraints excluded: chain U residue   93 VAL
Chi-restraints excluded: chain U residue   98 VAL
Chi-restraints excluded: chain U residue  101 VAL
Chi-restraints excluded: chain U residue  173 GLU
Chi-restraints excluded: chain U residue  200 VAL
Chi-restraints excluded: chain U residue  305 THR
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  173 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  310 ASP
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain D residue   20 ILE
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  173 GLU
Chi-restraints excluded: chain D residue  200 VAL
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   98 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 GLU
Chi-restraints excluded: chain E residue  200 VAL
Chi-restraints excluded: chain E residue  305 THR
Chi-restraints excluded: chain E residue  310 ASP
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   93 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  173 GLU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  310 ASP
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   91 LEU
Chi-restraints excluded: chain G residue   93 VAL
Chi-restraints excluded: chain G residue   98 VAL
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  173 GLU
Chi-restraints excluded: chain G residue  200 VAL
Chi-restraints excluded: chain G residue  305 THR
Chi-restraints excluded: chain G residue  310 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 232 optimal weight:    0.9990
   chunk 118 optimal weight:    0.8980
   chunk 147 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 201 optimal weight:    0.9980
   chunk 127 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
G  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.172964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.128659 restraints weight = 23171.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 3.19
r_work: 0.3070 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20792  Z= 0.090
  Angle     :  0.408   5.335  28072  Z= 0.217
  Chirality :  0.038   0.125   3136
  Planarity :  0.003   0.027   3552
  Dihedral  :  3.511  11.855   2680
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.21 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.17), residues: 2488
  helix:  1.61 (0.17), residues: 1008
  sheet: -0.77 (0.27), residues: 280
  loop : -2.02 (0.16), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  60 
 TYR   0.006   0.001   TYR A 226 
 PHE   0.007   0.001   PHE C  77 
 TRP   0.006   0.001   TRP B 167 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (20792)
  covalent geometry    : angle       0.40835 (28072)
  hydrogen bonds       : bond        0.02790 (  752)
  hydrogen bonds       : angle       3.86095 ( 2112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4386.31 seconds
wall clock time: 76 minutes 0.77 seconds (4560.77 seconds total)