Starting phenix.real_space_refine
on Mon Apr  6 07:19:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jzl_61917/04_2026/9jzl_61917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jzl_61917/04_2026/9jzl_61917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jzl_61917/04_2026/9jzl_61917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jzl_61917/04_2026/9jzl_61917.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jzl_61917/04_2026/9jzl_61917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jzl_61917/04_2026/9jzl_61917.map"
  }
  resolution = 3.21
  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=   0.004 sd=   0.089
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      48      5.49       5
     S      84      5.16       5
     C   10570      2.51       5
     N    2814      2.21       5
     O    3322      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16838
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2634
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 19, 'TRANS': 319}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2664
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 19, 'TRANS': 323}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2641
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 19, 'TRANS': 320}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 480
          Classifications: {'RNA': 24}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 3, 'rna3p': 20}
  Restraints were copied for chains:
    D, E, F, G
  Time building chain proxies: 4.36, per 1000 atoms: 0.26
  Number of scatterers: 16838
  At special positions: 0
  Unit cell: (134.922, 134.922, 100.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      84     16.00
     P      48     15.00
     O    3322      8.00
     N    2814      7.00
     C   10570      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: 1.46
  Conformation dependent library (CDL) restraints added in 765.1 milliseconds
  

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3800

  Finding SS restraints...
    Secondary structure from input PDB file:
      122 helices and 6 sheets defined
      67.0% alpha, 1.3% beta
      0 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 62 through 69
      removed outlier: 3.525A  pdb=" N   ARG A  66 " --> pdb=" O   ASP A  62 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   MET A  68 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE A  69 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 83
      removed outlier: 4.722A  pdb=" N   SER A  75 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 94
      removed outlier: 3.893A  pdb=" N   ALA A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 150
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 159 through 173
      removed outlier: 3.631A  pdb=" N   LYS A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 182
      removed outlier: 3.587A  pdb=" N   GLY A 179 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 202 through 213
    Processing helix  chain 'A' and resid 216 through 231
      removed outlier: 3.842A  pdb=" N   GLU A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 250 through 254
      removed outlier: 4.058A  pdb=" N   LEU A 253 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 277
    Processing helix  chain 'A' and resid 278 through 283
      Proline residue:  A 281  - end of helix
      No H-bonds generated for 'chain 'A' and resid 278 through 283'
    Processing helix  chain 'A' and resid 288 through 298
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 299 through 314
      removed outlier: 3.665A  pdb=" N   LYS A 312 " --> pdb=" O   TYR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 320
    Processing helix  chain 'A' and resid 332 through 342
      removed outlier: 3.921A  pdb=" N   ARG A 342 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 52 through 61
    Processing helix  chain 'B' and resid 62 through 69
      removed outlier: 3.794A  pdb=" N   ARG B  66 " --> pdb=" O   ASP B  62 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   MET B  68 " --> pdb=" O   SER B  64 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   PHE B  69 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 83
      removed outlier: 4.633A  pdb=" N   SER B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 3.802A  pdb=" N   ALA B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 150
      removed outlier: 3.769A  pdb=" N   GLY B 146 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 159 through 173
      removed outlier: 3.939A  pdb=" N   LYS B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
    Processing helix  chain 'B' and resid 190 through 200
    Processing helix  chain 'B' and resid 202 through 212
    Processing helix  chain 'B' and resid 216 through 231
      removed outlier: 3.786A  pdb=" N   GLU B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 248
    Processing helix  chain 'B' and resid 250 through 254
      removed outlier: 4.023A  pdb=" N   LEU B 253 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 276
      removed outlier: 3.548A  pdb=" N   ARG B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP B 264 " --> pdb=" O   TYR B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 283
    Processing helix  chain 'B' and resid 288 through 295
    Processing helix  chain 'B' and resid 299 through 314
    Processing helix  chain 'B' and resid 315 through 320
    Processing helix  chain 'B' and resid 332 through 342
      removed outlier: 4.127A  pdb=" N   ARG B 342 " --> pdb=" O   ARG B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 365
    Processing helix  chain 'C' and resid 49 through 51
      No H-bonds generated for 'chain 'C' and resid 49 through 51'
    Processing helix  chain 'C' and resid 52 through 61
      removed outlier: 3.583A  pdb=" N   ALA C  57 " --> pdb=" O   ILE C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 69
      removed outlier: 3.597A  pdb=" N   PHE C  69 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 83
      removed outlier: 4.470A  pdb=" N   SER C  75 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 93
      removed outlier: 3.786A  pdb=" N   ALA C  89 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 150
    Processing helix  chain 'C' and resid 152 through 157
    Processing helix  chain 'C' and resid 159 through 173
      removed outlier: 3.608A  pdb=" N   LYS C 163 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 182
    Processing helix  chain 'C' and resid 190 through 200
    Processing helix  chain 'C' and resid 202 through 212
    Processing helix  chain 'C' and resid 216 through 231
      removed outlier: 3.759A  pdb=" N   GLU C 221 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 248
    Processing helix  chain 'C' and resid 255 through 276
      removed outlier: 3.706A  pdb=" N   ARG C 263 " --> pdb=" O   ALA C 259 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP C 264 " --> pdb=" O   TYR C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 283
    Processing helix  chain 'C' and resid 288 through 295
    Processing helix  chain 'C' and resid 299 through 314
    Processing helix  chain 'C' and resid 315 through 320
    Processing helix  chain 'C' and resid 332 through 342
      removed outlier: 3.887A  pdb=" N   ARG C 342 " --> pdb=" O   ARG C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 354 through 365
    Processing helix  chain 'D' and resid 52 through 61
    Processing helix  chain 'D' and resid 62 through 69
      removed outlier: 3.525A  pdb=" N   ARG D  66 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   MET D  68 " --> pdb=" O   SER D  64 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE D  69 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 83
      removed outlier: 4.722A  pdb=" N   SER D  75 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 94
      removed outlier: 3.893A  pdb=" N   ALA D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 150
    Processing helix  chain 'D' and resid 152 through 157
    Processing helix  chain 'D' and resid 159 through 173
      removed outlier: 3.631A  pdb=" N   LYS D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 182
      removed outlier: 3.587A  pdb=" N   GLY D 179 " --> pdb=" O   ARG D 175 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU D 180 " --> pdb=" O   PRO D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 200
    Processing helix  chain 'D' and resid 202 through 213
    Processing helix  chain 'D' and resid 216 through 231
      removed outlier: 3.842A  pdb=" N   GLU D 221 " --> pdb=" O   SER D 217 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE D 222 " --> pdb=" O   PRO D 218 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 235 through 245
    Processing helix  chain 'D' and resid 250 through 254
      removed outlier: 4.058A  pdb=" N   LEU D 253 " --> pdb=" O   ASP D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 277
    Processing helix  chain 'D' and resid 278 through 283
      Proline residue:  D 281  - end of helix
      No H-bonds generated for 'chain 'D' and resid 278 through 283'
    Processing helix  chain 'D' and resid 288 through 298
      Proline residue:  D 296  - end of helix
    Processing helix  chain 'D' and resid 299 through 314
      removed outlier: 3.665A  pdb=" N   LYS D 312 " --> pdb=" O   TYR D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 315 through 320
    Processing helix  chain 'D' and resid 332 through 342
      removed outlier: 3.921A  pdb=" N   ARG D 342 " --> pdb=" O   ARG D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 354 through 365
    Processing helix  chain 'E' and resid 49 through 51
      No H-bonds generated for 'chain 'E' and resid 49 through 51'
    Processing helix  chain 'E' and resid 52 through 61
    Processing helix  chain 'E' and resid 62 through 69
      removed outlier: 3.794A  pdb=" N   ARG E  66 " --> pdb=" O   ASP E  62 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   MET E  68 " --> pdb=" O   SER E  64 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   PHE E  69 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 83
      removed outlier: 4.633A  pdb=" N   SER E  75 " --> pdb=" O   THR E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 93
      removed outlier: 3.802A  pdb=" N   ALA E  89 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 150
      removed outlier: 3.769A  pdb=" N   GLY E 146 " --> pdb=" O   SER E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 152 through 157
    Processing helix  chain 'E' and resid 159 through 173
      removed outlier: 3.939A  pdb=" N   LYS E 163 " --> pdb=" O   ALA E 159 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 177 through 182
    Processing helix  chain 'E' and resid 190 through 200
    Processing helix  chain 'E' and resid 202 through 212
    Processing helix  chain 'E' and resid 216 through 231
      removed outlier: 3.786A  pdb=" N   GLU E 221 " --> pdb=" O   SER E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 235 through 248
    Processing helix  chain 'E' and resid 250 through 254
      removed outlier: 4.023A  pdb=" N   LEU E 253 " --> pdb=" O   ASP E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 255 through 276
      removed outlier: 3.548A  pdb=" N   ARG E 263 " --> pdb=" O   ALA E 259 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP E 264 " --> pdb=" O   TYR E 260 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 279 through 283
    Processing helix  chain 'E' and resid 288 through 295
    Processing helix  chain 'E' and resid 299 through 314
    Processing helix  chain 'E' and resid 315 through 320
    Processing helix  chain 'E' and resid 332 through 342
      removed outlier: 4.127A  pdb=" N   ARG E 342 " --> pdb=" O   ARG E 338 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 354 through 365
    Processing helix  chain 'F' and resid 49 through 51
      No H-bonds generated for 'chain 'F' and resid 49 through 51'
    Processing helix  chain 'F' and resid 52 through 61
      removed outlier: 3.583A  pdb=" N   ALA F  57 " --> pdb=" O   ILE F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 69
      removed outlier: 3.597A  pdb=" N   PHE F  69 " --> pdb=" O   ARG F  65 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 71 through 83
      removed outlier: 4.470A  pdb=" N   SER F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 93
      removed outlier: 3.786A  pdb=" N   ALA F  89 " --> pdb=" O   GLY F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 150
    Processing helix  chain 'F' and resid 152 through 157
    Processing helix  chain 'F' and resid 159 through 173
      removed outlier: 3.608A  pdb=" N   LYS F 163 " --> pdb=" O   ALA F 159 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 182
    Processing helix  chain 'F' and resid 190 through 200
    Processing helix  chain 'F' and resid 202 through 212
    Processing helix  chain 'F' and resid 216 through 231
      removed outlier: 3.759A  pdb=" N   GLU F 221 " --> pdb=" O   SER F 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 235 through 248
    Processing helix  chain 'F' and resid 255 through 276
      removed outlier: 3.706A  pdb=" N   ARG F 263 " --> pdb=" O   ALA F 259 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP F 264 " --> pdb=" O   TYR F 260 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 279 through 283
    Processing helix  chain 'F' and resid 288 through 295
    Processing helix  chain 'F' and resid 299 through 314
    Processing helix  chain 'F' and resid 315 through 320
    Processing helix  chain 'F' and resid 332 through 342
      removed outlier: 3.887A  pdb=" N   ARG F 342 " --> pdb=" O   ARG F 338 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 354 through 365
    Processing sheet with id=1, first strand: chain 'A' and resid 99 through 100
    Processing sheet with id=2, first strand: chain 'B' and resid 99 through 105
      removed outlier: 3.613A  pdb=" N   LEU B 101 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL B 113 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'C' and resid 99 through 100
    Processing sheet with id=4, first strand: chain 'D' and resid 99 through 100
    Processing sheet with id=5, first strand: chain 'E' and resid 99 through 105
      removed outlier: 3.613A  pdb=" N   LEU E 101 " --> pdb=" O   VAL E 113 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL E 113 " --> pdb=" O   LEU E 101 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'F' and resid 99 through 100

    840 hydrogen bonds defined for protein.
    2322 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 2.53

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3354
        1.33 -     1.46: 4956
        1.46 -     1.58: 8736
        1.58 -     1.70: 96
        1.70 -     1.83: 144
  Bond restraints: 17286
  Sorted by residual:
  bond pdb=" CA  SER B 304 "
       pdb=" CB  SER B 304 "
    ideal  model  delta    sigma   weight residual
    1.530  1.461  0.069 1.56e-02 4.11e+03 1.94e+01
  bond pdb=" CA  SER E 304 "
       pdb=" CB  SER E 304 "
    ideal  model  delta    sigma   weight residual
    1.530  1.461  0.069 1.56e-02 4.11e+03 1.94e+01
  bond pdb=" CA  SER B 152 "
       pdb=" CB  SER B 152 "
    ideal  model  delta    sigma   weight residual
    1.536  1.469  0.068 1.58e-02 4.01e+03 1.83e+01
  bond pdb=" CA  SER E 152 "
       pdb=" CB  SER E 152 "
    ideal  model  delta    sigma   weight residual
    1.536  1.469  0.068 1.58e-02 4.01e+03 1.83e+01
  bond pdb=" CE1 HIS D 139 "
       pdb=" NE2 HIS D 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.363 -0.042 1.00e-02 1.00e+04 1.78e+01
  ... (remaining 17281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 19584
        2.05 -     4.11: 3554
        4.11 -     6.16: 382
        6.16 -     8.21: 54
        8.21 -    10.27: 18
  Bond angle restraints: 23592
  Sorted by residual:
  angle pdb=" CA  THR B 236 "
        pdb=" CB  THR B 236 "
        pdb=" OG1 THR B 236 "
      ideal   model   delta    sigma   weight residual
     109.60   99.33   10.27 1.50e+00 4.44e-01 4.68e+01
  angle pdb=" CA  THR E 236 "
        pdb=" CB  THR E 236 "
        pdb=" OG1 THR E 236 "
      ideal   model   delta    sigma   weight residual
     109.60   99.33   10.27 1.50e+00 4.44e-01 4.68e+01
  angle pdb=" CA  THR C 236 "
        pdb=" CB  THR C 236 "
        pdb=" OG1 THR C 236 "
      ideal   model   delta    sigma   weight residual
     109.60  100.18    9.42 1.50e+00 4.44e-01 3.94e+01
  angle pdb=" CA  THR F 236 "
        pdb=" CB  THR F 236 "
        pdb=" OG1 THR F 236 "
      ideal   model   delta    sigma   weight residual
     109.60  100.18    9.42 1.50e+00 4.44e-01 3.94e+01
  angle pdb=" CA  THR D 236 "
        pdb=" CB  THR D 236 "
        pdb=" OG1 THR D 236 "
      ideal   model   delta    sigma   weight residual
     109.60  100.48    9.12 1.50e+00 4.44e-01 3.70e+01
  ... (remaining 23587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.26: 9482
       15.26 -    30.53: 748
       30.53 -    45.79: 184
       45.79 -    61.05: 110
       61.05 -    76.32: 50
  Dihedral angle restraints: 10574
    sinusoidal: 4682
      harmonic: 5892
  Sorted by residual:
  dihedral pdb=" CA  ARG F  54 "
           pdb=" C   ARG F  54 "
           pdb=" N   GLN F  55 "
           pdb=" CA  GLN F  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ARG C  54 "
           pdb=" C   ARG C  54 "
           pdb=" N   GLN C  55 "
           pdb=" CA  GLN C  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  LYS B 117 "
           pdb=" C   LYS B 117 "
           pdb=" N   PHE B 118 "
           pdb=" CA  PHE B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.22  -16.78     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 10571 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1660
       0.082 -    0.164: 764
       0.164 -    0.246: 260
       0.246 -    0.328: 38
       0.328 -    0.410: 2
  Chirality restraints: 2724
  Sorted by residual:
  chirality pdb=" C3'   U G  24 "
            pdb=" C4'   U G  24 "
            pdb=" O3'   U G  24 "
            pdb=" C2'   U G  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.89    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C3'   U R  24 "
            pdb=" C4'   U R  24 "
            pdb=" O3'   U R  24 "
            pdb=" C2'   U R  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.89    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" P     U R   1 "
            pdb=" OP1   U R   1 "
            pdb=" OP2   U R   1 "
            pdb=" O5'   U R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.72   -0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 2721 not shown)

  Planarity restraints: 2850
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 341 "   -0.531 9.50e-02 1.11e+02   2.38e-01 3.68e+01
        pdb=" NE  ARG F 341 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 341 "    0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 341 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 341 "    0.531 9.50e-02 1.11e+02   2.38e-01 3.68e+01
        pdb=" NE  ARG C 341 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 341 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 341 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 341 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 263 "   -0.431 9.50e-02 1.11e+02   1.93e-01 2.33e+01
        pdb=" NE  ARG B 263 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 263 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 263 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 263 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2847 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 6666
        2.91 -     3.40: 17176
        3.40 -     3.90: 28312
        3.90 -     4.40: 32622
        4.40 -     4.90: 51616
  Nonbonded interactions: 136392
  Sorted by model distance:
  nonbonded pdb=" O   ALA F 251 "
            pdb=" OG1 THR F 254 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" O   ALA C 251 "
            pdb=" OG1 THR C 254 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" OD1 ASP E 250 "
            pdb=" OG1 THR E 252 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" OD1 ASP B 250 "
            pdb=" OG1 THR B 252 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" OG1 THR C  37 "
            pdb=" O   LEU D 128 "
     model   vdw
     2.430 3.040
  ... (remaining 136387 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'R'
  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=0.16 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:             0.070
  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:          0.230
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     17.380
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
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      :  0.011   0.069  17286  Z= 0.682
  Angle     :  1.599  10.267  23592  Z= 1.070
  Chirality :  0.100   0.410   2724
  Planarity :  0.017   0.238   2850
  Dihedral  : 14.162  76.317   6774
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  8.02 %
    Favored  : 91.86 %
  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: -1.85 (0.16), residues: 2020
  helix: -0.99 (0.13), residues: 1140
  sheet:  None (None), residues: 0
  loop : -1.40 (0.18), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.004   ARG F 341 
 TYR   0.054   0.010   TYR B 339 
 PHE   0.050   0.009   PHE C 118 
 TRP   0.053   0.015   TRP B 196 
 HIS   0.018   0.005   HIS E  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.01113 (17286)
  covalent geometry    : angle       1.59867 (23592)
  hydrogen bonds       : bond        0.19895 (  840)
  hydrogen bonds       : angle       7.08817 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7422 (ptp-170)
REVERT: A  352 GLU cc_start: 0.9337 (tt0) cc_final: 0.8980 (pm20)
REVERT: B  235 MET cc_start: 0.9107 (mtp) cc_final: 0.8900 (ttm)
REVERT: B  244 TYR cc_start: 0.9018 (t80) cc_final: 0.8539 (t80)
REVERT: B  352 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8383 (mp0)
REVERT: C  186 GLN cc_start: 0.9478 (tt0) cc_final: 0.9231 (tm-30)
REVERT: D  126 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7464 (ptp-170)
REVERT: D  352 GLU cc_start: 0.9351 (tt0) cc_final: 0.9080 (pm20)
REVERT: E  160 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9121 (tp30)
REVERT: E  244 TYR cc_start: 0.8988 (t80) cc_final: 0.8521 (t80)
REVERT: E  352 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8324 (mp0)
REVERT: F  186 GLN cc_start: 0.9444 (tt0) cc_final: 0.9037 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 209
  average time/residue: 0.1615
  time to fit residues: 47.1795
Evaluate side-chains
  127 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain E residue  113 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 200 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 GLN
B 178 HIS
C 301 ASN
C 314 ASN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 335 GLN
E 178 HIS
F 301 ASN
F 314 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.083436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.064033 restraints weight = 40685.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.34
r_work: 0.2788 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17286  Z= 0.126
  Angle     :  0.529   7.468  23592  Z= 0.269
  Chirality :  0.038   0.132   2724
  Planarity :  0.003   0.032   2850
  Dihedral  : 10.081  59.997   2958
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  9.36 %
    Favored  : 90.00 %
  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:  1.00 (0.18), residues: 2020
  helix:  1.55 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.54 (0.20), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 340 
 TYR   0.015   0.002   TYR F 308 
 PHE   0.011   0.001   PHE D 222 
 TRP   0.012   0.001   TRP C 309 
 HIS   0.005   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (17286)
  covalent geometry    : angle       0.52938 (23592)
  hydrogen bonds       : bond        0.04665 (  840)
  hydrogen bonds       : angle       4.37623 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.611 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7400 (ptm160)
REVERT: B  170 MET cc_start: 0.8841 (mmm) cc_final: 0.8634 (mmm)
REVERT: B  189 ASN cc_start: 0.8595 (m-40) cc_final: 0.8162 (t0)
REVERT: C  317 MET cc_start: 0.8902 (mmm) cc_final: 0.8599 (mmm)
REVERT: C  321 ARG cc_start: 0.8866 (mtp85) cc_final: 0.8652 (mtp85)
REVERT: D  126 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7237 (ptp-170)
REVERT: D  186 GLN cc_start: 0.8945 (pp30) cc_final: 0.8361 (pm20)
REVERT: E  170 MET cc_start: 0.8834 (mmm) cc_final: 0.8480 (mmm)
REVERT: E  189 ASN cc_start: 0.8779 (m-40) cc_final: 0.8305 (t0)
REVERT: F  317 MET cc_start: 0.8899 (mmm) cc_final: 0.8593 (mmm)
REVERT: F  321 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8661 (mtp85)
  outliers start: 11
  outliers final: 4
  residues processed: 146
  average time/residue: 0.1431
  time to fit residues: 31.0526
Evaluate side-chains
  120 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain E residue   61 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 128 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 169 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 139 optimal weight:   20.0000
   chunk 150 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 84 optimal weight:    9.9990
   chunk 180 optimal weight:   10.0000
   chunk 155 optimal weight:    5.9990
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 GLN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.077146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.057628 restraints weight = 42759.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 3.48
r_work: 0.2653 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  17286  Z= 0.266
  Angle     :  0.617   6.854  23592  Z= 0.316
  Chirality :  0.043   0.146   2724
  Planarity :  0.004   0.039   2850
  Dihedral  : 10.178  59.923   2956
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.23 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.04 (0.19), residues: 2020
  helix:  1.47 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.34 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 165 
 TYR   0.020   0.002   TYR B 244 
 PHE   0.014   0.002   PHE E 282 
 TRP   0.007   0.001   TRP F 309 
 HIS   0.006   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (17286)
  covalent geometry    : angle       0.61713 (23592)
  hydrogen bonds       : bond        0.05937 (  840)
  hydrogen bonds       : angle       4.56567 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7879 (ptm160) cc_final: 0.6967 (ptp-170)
REVERT: B  189 ASN cc_start: 0.8814 (m-40) cc_final: 0.8420 (t0)
REVERT: C  321 ARG cc_start: 0.8992 (mtp85) cc_final: 0.8779 (mtp85)
REVERT: D  126 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7128 (ptp-170)
REVERT: E  189 ASN cc_start: 0.8812 (m-40) cc_final: 0.8411 (t0)
REVERT: F  321 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8695 (mtp85)
  outliers start: 34
  outliers final: 26
  residues processed: 137
  average time/residue: 0.1318
  time to fit residues: 27.5323
Evaluate side-chains
  124 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  364 ILE
Chi-restraints excluded: chain F residue   53 ILE
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 173 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 GLN
D  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.080948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.061478 restraints weight = 41973.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 3.46
r_work: 0.2732 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2738 r_free = 0.2738    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2738 r_free = 0.2738    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17286  Z= 0.124
  Angle     :  0.494   8.506  23592  Z= 0.248
  Chirality :  0.038   0.143   2724
  Planarity :  0.003   0.035   2850
  Dihedral  :  9.992  60.003   2956
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.51 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.19), residues: 2020
  helix:  1.90 (0.16), residues: 1164
  sheet:  None (None), residues: 0
  loop : -0.08 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 321 
 TYR   0.012   0.001   TYR A 244 
 PHE   0.007   0.001   PHE D  90 
 TRP   0.010   0.001   TRP F 309 
 HIS   0.004   0.001   HIS D 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (17286)
  covalent geometry    : angle       0.49419 (23592)
  hydrogen bonds       : bond        0.04066 (  840)
  hydrogen bonds       : angle       4.03047 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7257 (ptm160)
REVERT: B  170 MET cc_start: 0.8642 (mmm) cc_final: 0.7977 (mmm)
REVERT: B  189 ASN cc_start: 0.8822 (m-40) cc_final: 0.8328 (t0)
REVERT: D  100 TYR cc_start: 0.8091 (m-10) cc_final: 0.7682 (m-10)
REVERT: D  126 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7250 (ptm160)
REVERT: D  186 GLN cc_start: 0.9415 (pt0) cc_final: 0.8933 (pp30)
REVERT: E  170 MET cc_start: 0.8645 (mmm) cc_final: 0.7958 (mmm)
REVERT: E  189 ASN cc_start: 0.8828 (m-40) cc_final: 0.8327 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 139
  average time/residue: 0.1292
  time to fit residues: 27.3635
Evaluate side-chains
  123 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 162 optimal weight:    0.1980
   chunk 184 optimal weight:    0.0570
   chunk 15 optimal weight:   20.0000
   chunk 117 optimal weight:    8.9990
   chunk 107 optimal weight:    9.9990
   chunk 190 optimal weight:    7.9990
   chunk 203 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 73 optimal weight:   20.0000
   chunk 89 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   overall best weight:    3.0504

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.080860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.061557 restraints weight = 41286.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 3.38
r_work: 0.2741 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  17286  Z= 0.115
  Angle     :  0.490   9.318  23592  Z= 0.242
  Chirality :  0.037   0.141   2724
  Planarity :  0.003   0.033   2850
  Dihedral  :  9.918  59.952   2956
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.50 %
    Favored  : 86.10 %
  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:  1.74 (0.19), residues: 2020
  helix:  2.01 (0.16), residues: 1162
  sheet:  None (None), residues: 0
  loop :  0.02 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 321 
 TYR   0.012   0.001   TYR A 244 
 PHE   0.008   0.001   PHE A 222 
 TRP   0.008   0.001   TRP F 309 
 HIS   0.003   0.001   HIS D 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (17286)
  covalent geometry    : angle       0.48962 (23592)
  hydrogen bonds       : bond        0.03945 (  840)
  hydrogen bonds       : angle       3.92852 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7315 (ptm160)
REVERT: B  189 ASN cc_start: 0.8856 (m-40) cc_final: 0.8269 (t0)
REVERT: C  321 ARG cc_start: 0.8772 (mtp85) cc_final: 0.8542 (mtp-110)
REVERT: D  100 TYR cc_start: 0.8244 (m-10) cc_final: 0.7890 (m-10)
REVERT: D  126 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7297 (ptm160)
REVERT: D  186 GLN cc_start: 0.9385 (pt0) cc_final: 0.8791 (pp30)
REVERT: E  189 ASN cc_start: 0.8853 (m-40) cc_final: 0.8328 (t0)
REVERT: E  321 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8252 (mmp80)
REVERT: F  321 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8529 (mtp-110)
  outliers start: 24
  outliers final: 16
  residues processed: 138
  average time/residue: 0.1218
  time to fit residues: 26.0449
Evaluate side-chains
  128 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 142 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 102 optimal weight:   20.0000
   chunk 193 optimal weight:    5.9990
   chunk 196 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 147 optimal weight:    7.9990
   chunk 114 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   overall best weight:    4.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.079264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.059957 restraints weight = 41766.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 3.42
r_work: 0.2708 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  17286  Z= 0.162
  Angle     :  0.516   7.223  23592  Z= 0.256
  Chirality :  0.038   0.146   2724
  Planarity :  0.003   0.035   2850
  Dihedral  :  9.921  59.923   2956
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.09 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.19), residues: 2020
  helix:  1.91 (0.15), residues: 1164
  sheet:  None (None), residues: 0
  loop :  0.01 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 321 
 TYR   0.012   0.001   TYR A 244 
 PHE   0.007   0.001   PHE B 282 
 TRP   0.007   0.001   TRP F 309 
 HIS   0.003   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (17286)
  covalent geometry    : angle       0.51633 (23592)
  hydrogen bonds       : bond        0.04412 (  840)
  hydrogen bonds       : angle       4.05166 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
REVERT: B  189 ASN cc_start: 0.8877 (m-40) cc_final: 0.8351 (t0)
REVERT: C  321 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8515 (mtp-110)
REVERT: D  100 TYR cc_start: 0.8266 (m-10) cc_final: 0.7953 (m-10)
REVERT: D  126 ARG cc_start: 0.8072 (ptm160) cc_final: 0.7240 (ptm160)
REVERT: D  186 GLN cc_start: 0.9426 (pt0) cc_final: 0.8820 (pp30)
REVERT: E  189 ASN cc_start: 0.8886 (m-40) cc_final: 0.8348 (t0)
REVERT: E  321 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8261 (mmp80)
REVERT: F  250 ASP cc_start: 0.8709 (m-30) cc_final: 0.8506 (m-30)
REVERT: F  321 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8520 (mtp-110)
  outliers start: 32
  outliers final: 22
  residues processed: 137
  average time/residue: 0.1200
  time to fit residues: 25.3601
Evaluate side-chains
  132 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  364 ILE
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 166 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 135 optimal weight:    4.9990
   chunk 181 optimal weight:    0.9990
   chunk 112 optimal weight:   20.0000
   chunk 122 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 69 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 204 optimal weight:   20.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.078680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.059389 restraints weight = 41543.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.40
r_work: 0.2696 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  17286  Z= 0.177
  Angle     :  0.539  10.814  23592  Z= 0.266
  Chirality :  0.039   0.148   2724
  Planarity :  0.004   0.037   2850
  Dihedral  :  9.940  59.914   2956
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.50 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.57 (0.19), residues: 2020
  helix:  1.85 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.02 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 321 
 TYR   0.014   0.001   TYR E 244 
 PHE   0.008   0.001   PHE E 282 
 TRP   0.007   0.001   TRP F 309 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (17286)
  covalent geometry    : angle       0.53920 (23592)
  hydrogen bonds       : bond        0.04564 (  840)
  hydrogen bonds       : angle       4.10206 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A  186 GLN cc_start: 0.9398 (tt0) cc_final: 0.8977 (pp30)
REVERT: B  189 ASN cc_start: 0.8874 (m-40) cc_final: 0.8312 (t0)
REVERT: C  321 ARG cc_start: 0.8806 (mtp85) cc_final: 0.8525 (mtp-110)
REVERT: D  126 ARG cc_start: 0.8078 (ptm160) cc_final: 0.7243 (ptm160)
REVERT: D  186 GLN cc_start: 0.9421 (pt0) cc_final: 0.8867 (pp30)
REVERT: E  189 ASN cc_start: 0.8873 (m-40) cc_final: 0.8314 (t0)
REVERT: E  321 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8328 (mmp80)
REVERT: F  321 ARG cc_start: 0.8803 (mtp85) cc_final: 0.8524 (mtp-110)
  outliers start: 34
  outliers final: 27
  residues processed: 138
  average time/residue: 0.1255
  time to fit residues: 26.6567
Evaluate side-chains
  135 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  354 SER
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  364 ILE
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 200 optimal weight:    7.9990
   chunk 202 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 134 optimal weight:   20.0000
   chunk 80 optimal weight:    4.9990
   chunk 159 optimal weight:    6.9990
   chunk 114 optimal weight:    0.8980
   chunk 125 optimal weight:    2.9990
   chunk 138 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    4.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.079122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.059857 restraints weight = 41792.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 3.37
r_work: 0.2708 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  17286  Z= 0.156
  Angle     :  0.531   9.405  23592  Z= 0.259
  Chirality :  0.038   0.146   2724
  Planarity :  0.003   0.035   2850
  Dihedral  :  9.926  59.910   2956
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.33 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.19), residues: 2020
  helix:  1.88 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.03 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 321 
 TYR   0.013   0.001   TYR D 244 
 PHE   0.007   0.001   PHE B 282 
 TRP   0.008   0.001   TRP F 309 
 HIS   0.003   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (17286)
  covalent geometry    : angle       0.53128 (23592)
  hydrogen bonds       : bond        0.04330 (  840)
  hydrogen bonds       : angle       4.02970 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  186 GLN cc_start: 0.9390 (tt0) cc_final: 0.9027 (pp30)
REVERT: B  189 ASN cc_start: 0.8900 (m-40) cc_final: 0.8361 (t0)
REVERT: D   55 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8821 (mm110)
REVERT: D  126 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7322 (ptm160)
REVERT: D  186 GLN cc_start: 0.9441 (pt0) cc_final: 0.8885 (pp30)
REVERT: E  170 MET cc_start: 0.8701 (mmm) cc_final: 0.8453 (mmt)
REVERT: E  189 ASN cc_start: 0.8906 (m-40) cc_final: 0.8368 (t0)
REVERT: E  321 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8340 (mmp80)
REVERT: F  321 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8606 (mtp-110)
  outliers start: 34
  outliers final: 26
  residues processed: 138
  average time/residue: 0.1182
  time to fit residues: 25.2258
Evaluate side-chains
  136 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue   55 GLN
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  354 SER
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 67 optimal weight:   20.0000
   chunk 39 optimal weight:   10.0000
   chunk 9 optimal weight:   30.0000
   chunk 90 optimal weight:    3.9990
   chunk 191 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:   20.0000
   chunk 113 optimal weight:    1.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.080214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.060935 restraints weight = 41404.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 3.41
r_work: 0.2732 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17286  Z= 0.123
  Angle     :  0.518   9.118  23592  Z= 0.250
  Chirality :  0.037   0.144   2724
  Planarity :  0.003   0.033   2850
  Dihedral  :  9.901  59.921   2956
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.79 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.71 (0.19), residues: 2020
  helix:  1.98 (0.15), residues: 1160
  sheet:  None (None), residues: 0
  loop :  0.01 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 321 
 TYR   0.011   0.001   TYR D 244 
 PHE   0.006   0.001   PHE A  90 
 TRP   0.009   0.001   TRP F 309 
 HIS   0.003   0.001   HIS D 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (17286)
  covalent geometry    : angle       0.51798 (23592)
  hydrogen bonds       : bond        0.03922 (  840)
  hydrogen bonds       : angle       3.92146 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  186 GLN cc_start: 0.9408 (tt0) cc_final: 0.9033 (pp30)
REVERT: B  189 ASN cc_start: 0.8888 (m-40) cc_final: 0.8268 (t0)
REVERT: D   55 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8805 (mm110)
REVERT: D  126 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7337 (ptm160)
REVERT: D  186 GLN cc_start: 0.9443 (pt0) cc_final: 0.8885 (pp30)
REVERT: E  170 MET cc_start: 0.8609 (mmm) cc_final: 0.7874 (mmm)
REVERT: E  189 ASN cc_start: 0.8877 (m-40) cc_final: 0.8286 (t0)
REVERT: E  321 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8302 (mmp80)
  outliers start: 29
  outliers final: 25
  residues processed: 141
  average time/residue: 0.1228
  time to fit residues: 27.0045
Evaluate side-chains
  139 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  354 SER
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue   55 GLN
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  249 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 143 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 58 optimal weight:    0.0980
   chunk 65 optimal weight:   30.0000
   chunk 135 optimal weight:    7.9990
   chunk 175 optimal weight:    6.9990
   chunk 196 optimal weight:    1.9990
   chunk 8 optimal weight:   30.0000
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.081604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.062246 restraints weight = 41226.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 3.42
r_work: 0.2760 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  17286  Z= 0.104
  Angle     :  0.512   9.297  23592  Z= 0.246
  Chirality :  0.037   0.141   2724
  Planarity :  0.003   0.031   2850
  Dihedral  :  9.863  59.900   2956
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 13.37 %
    Favored  : 85.29 %
  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:  1.87 (0.19), residues: 2020
  helix:  2.13 (0.16), residues: 1158
  sheet:  None (None), residues: 0
  loop :  0.05 (0.22), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 321 
 TYR   0.011   0.001   TYR F 244 
 PHE   0.007   0.001   PHE A 222 
 TRP   0.010   0.001   TRP F 309 
 HIS   0.003   0.000   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (17286)
  covalent geometry    : angle       0.51229 (23592)
  hydrogen bonds       : bond        0.03588 (  840)
  hydrogen bonds       : angle       3.83102 ( 2322)

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

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

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4040 Ramachandran restraints generated.
    2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A  164 LYS cc_start: 0.8613 (tttm) cc_final: 0.8389 (tptm)
REVERT: A  186 GLN cc_start: 0.9357 (tt0) cc_final: 0.8945 (pp30)
REVERT: B  189 ASN cc_start: 0.8897 (m-40) cc_final: 0.8194 (t0)
REVERT: D   55 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8784 (mm110)
REVERT: D  126 ARG cc_start: 0.8112 (ptm160) cc_final: 0.7280 (ptm160)
REVERT: D  164 LYS cc_start: 0.8629 (tttm) cc_final: 0.8396 (tptm)
REVERT: D  186 GLN cc_start: 0.9468 (pt0) cc_final: 0.8848 (pp30)
REVERT: E  170 MET cc_start: 0.8585 (mmm) cc_final: 0.7833 (mmm)
REVERT: E  189 ASN cc_start: 0.8900 (m-40) cc_final: 0.8201 (t0)
REVERT: E  321 ARG cc_start: 0.8752 (mmm-85) cc_final: 0.8293 (mmp80)
  outliers start: 23
  outliers final: 21
  residues processed: 135
  average time/residue: 0.1198
  time to fit residues: 24.9979
Evaluate side-chains
  132 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain D residue   55 GLN
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  138 SER
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  249 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 146 optimal weight:    6.9990
   chunk 114 optimal weight:    9.9990
   chunk 69 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 168 optimal weight:   50.0000
   chunk 50 optimal weight:   10.0000
   chunk 138 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 158 optimal weight:    0.6980
   chunk 142 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    5.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.079013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.059695 restraints weight = 41327.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 3.40
r_work: 0.2703 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17286  Z= 0.172
  Angle     :  0.549   9.082  23592  Z= 0.268
  Chirality :  0.039   0.145   2724
  Planarity :  0.003   0.035   2850
  Dihedral  :  9.892  59.879   2956
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.26 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.66 (0.19), residues: 2020
  helix:  1.93 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop :  0.01 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 321 
 TYR   0.012   0.001   TYR D 244 
 PHE   0.007   0.001   PHE A 222 
 TRP   0.007   0.001   TRP C 309 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (17286)
  covalent geometry    : angle       0.54856 (23592)
  hydrogen bonds       : bond        0.04419 (  840)
  hydrogen bonds       : angle       4.03099 ( 2322)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3052.61 seconds
wall clock time: 53 minutes 18.78 seconds (3198.78 seconds total)