Starting phenix.real_space_refine
on Thu Aug  6 19:23:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jzl_61917/08_2026/9jzl_61917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jzl_61917/08_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jzl_61917/08_2026/9jzl_61917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jzl_61917/08_2026/9jzl_61917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jzl_61917/08_2026/9jzl_61917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jzl_61917/08_2026/9jzl_61917.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 4.77, per 1000 atoms: 0.28
  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: 1.51
  Conformation dependent library (CDL) restraints added in 575.6 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: 1.76
  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: 2.76

  Time building geometry restraints manager: 1.94 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: 19614
        2.05 -     4.11: 3534
        4.11 -     6.16: 376
        6.16 -     8.21: 50
        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: 1688
       0.082 -    0.164: 748
       0.164 -    0.246: 252
       0.246 -    0.328: 34
       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:             0.170
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.670
  Find NCS groups from input model:        0.130
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
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= 0.707
  Angle     :  1.593  10.267  23592  Z= 1.094
  Chirality :  0.099   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/Z
  covalent geometry    : bond        0.01111 /  0.71 (17286)
  covalent geometry    : angle       1.59277 /  1.09 (23592)
  hydrogen bonds       : bond        0.19895 / 13.55 (  840)
  hydrogen bonds       : angle       7.08817 /  5.16 ( 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  : 0.674 
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: 0.1655
  time to fit residues: 48.9841
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  : 0.639 
-------------------------------------------------------------------------------
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...
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 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 301 ASN
C 314 ASN
D  63 GLN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 335 GLN
E 178 HIS
** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 301 ASN
F 314 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.083628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.064218 restraints weight = 40622.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.35
r_work: 0.2792 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17286  Z= 0.133
  Angle     :  0.538   6.906  23592  Z= 0.279
  Chirality :  0.038   0.134   2724
  Planarity :  0.004   0.041   2850
  Dihedral  : 10.141  60.215   2958
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.36 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.18), residues: 2020
  helix:  1.47 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.53 (0.20), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 340 
 TYR   0.017   0.002   TYR C 308 
 PHE   0.008   0.001   PHE D 222 
 TRP   0.011   0.001   TRP C 309 
 HIS   0.004   0.001   HIS D 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (17286)
  covalent geometry    : angle       0.53803 /  0.28 (23592)
  hydrogen bonds       : bond        0.05021 /  3.43 (  840)
  hydrogen bonds       : angle       4.42510 /  3.21 ( 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
  152 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7164 (ptp-170)
REVERT: B  189 ASN cc_start: 0.8596 (m-40) cc_final: 0.8120 (t0)
REVERT: B  352 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8020 (mp0)
REVERT: C  321 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8649 (mtp85)
REVERT: D  126 ARG cc_start: 0.8001 (ptm160) cc_final: 0.7266 (ptp-170)
REVERT: D  187 MET cc_start: 0.9213 (ptt) cc_final: 0.8968 (ptt)
REVERT: E  170 MET cc_start: 0.8748 (mmm) cc_final: 0.8383 (mmm)
REVERT: E  189 ASN cc_start: 0.8791 (m-40) cc_final: 0.8287 (t0)
REVERT: E  235 MET cc_start: 0.8722 (mtm) cc_final: 0.8511 (mtp)
REVERT: E  352 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8012 (mp0)
REVERT: F  321 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8679 (mtp85)
  outliers start: 16
  outliers final: 6
  residues processed: 152
  average time/residue: 0.1356
  time to fit residues: 30.7635
Evaluate side-chains
  128 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  257 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:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 169 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 139 optimal weight:   20.0000
   chunk 150 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 180 optimal weight:   10.0000
   chunk 155 optimal weight:    0.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.080640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.061113 restraints weight = 41982.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 3.45
r_work: 0.2728 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  17286  Z= 0.160
  Angle     :  0.521   6.173  23592  Z= 0.267
  Chirality :  0.039   0.133   2724
  Planarity :  0.004   0.034   2850
  Dihedral  : 10.076  60.118   2956
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.17 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.19), residues: 2020
  helix:  1.81 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.20 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 175 
 TYR   0.014   0.002   TYR C 308 
 PHE   0.008   0.001   PHE E 282 
 TRP   0.008   0.001   TRP C 309 
 HIS   0.004   0.001   HIS E  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 (17286)
  covalent geometry    : angle       0.52109 /  0.27 (23592)
  hydrogen bonds       : bond        0.04865 /  3.34 (  840)
  hydrogen bonds       : angle       4.24203 /  3.07 ( 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
  148 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7101 (ptp-170)
REVERT: B  170 MET cc_start: 0.8688 (mmm) cc_final: 0.8101 (mmp)
REVERT: B  189 ASN cc_start: 0.8856 (m-40) cc_final: 0.8319 (t0)
REVERT: C  321 ARG cc_start: 0.8944 (mtp85) cc_final: 0.8681 (mtp85)
REVERT: D   63 GLN cc_start: 0.7776 (tp40) cc_final: 0.7541 (tp-100)
REVERT: D  126 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7152 (ptp-170)
REVERT: E  189 ASN cc_start: 0.8861 (m-40) cc_final: 0.8305 (t0)
REVERT: F  321 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8677 (mtp85)
  outliers start: 21
  outliers final: 14
  residues processed: 146
  average time/residue: 0.1232
  time to fit residues: 27.7050
Evaluate side-chains
  125 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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  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 D residue  112 VAL
Chi-restraints excluded: chain D residue  115 THR
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  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:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   chunk 173 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    6.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.078394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.058831 restraints weight = 42438.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 3.48
r_work: 0.2680 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2686 r_free = 0.2686    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  17286  Z= 0.214
  Angle     :  0.561   8.362  23592  Z= 0.285
  Chirality :  0.040   0.133   2724
  Planarity :  0.004   0.038   2850
  Dihedral  : 10.085  60.062   2956
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.34 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.19), residues: 2020
  helix:  1.67 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop : -0.14 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 321 
 TYR   0.018   0.002   TYR D 100 
 PHE   0.010   0.001   PHE E 282 
 TRP   0.008   0.001   TRP F 309 
 HIS   0.005   0.001   HIS B  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00506 /  0.21 (17286)
  covalent geometry    : angle       0.56104 /  0.28 (23592)
  hydrogen bonds       : bond        0.05136 /  3.53 (  840)
  hydrogen bonds       : angle       4.29466 /  3.11 ( 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: 30
    poor density    : 112
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7119 (ptm160)
REVERT: A  187 MET cc_start: 0.9235 (ptt) cc_final: 0.9034 (mpp)
REVERT: B  189 ASN cc_start: 0.8882 (m-40) cc_final: 0.8349 (t0)
REVERT: C  321 ARG cc_start: 0.8972 (mtp85) cc_final: 0.8753 (mtp85)
REVERT: D  126 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7071 (ptm160)
REVERT: E  170 MET cc_start: 0.8717 (mmm) cc_final: 0.8179 (mmp)
REVERT: E  189 ASN cc_start: 0.8884 (m-40) cc_final: 0.8338 (t0)
REVERT: F  321 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8752 (mtp85)
  outliers start: 30
  outliers final: 22
  residues processed: 136
  average time/residue: 0.1250
  time to fit residues: 26.0385
Evaluate side-chains
  129 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
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  217 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  112 VAL
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  115 THR
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   61 LEU
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  115 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 162 optimal weight:    7.9990
   chunk 184 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 117 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 190 optimal weight:    6.9990
   chunk 203 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 101 optimal weight:   30.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.078937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.059359 restraints weight = 42082.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 3.48
r_work: 0.2691 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17286  Z= 0.172
  Angle     :  0.521   9.124  23592  Z= 0.263
  Chirality :  0.039   0.131   2724
  Planarity :  0.004   0.038   2850
  Dihedral  : 10.030  60.061   2956
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.92 %
    Favored  : 86.16 %
  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:  1.48 (0.19), residues: 2020
  helix:  1.77 (0.15), residues: 1164
  sheet:  None (None), residues: 0
  loop : -0.06 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 321 
 TYR   0.013   0.001   TYR D 244 
 PHE   0.007   0.001   PHE E 282 
 TRP   0.009   0.001   TRP C 309 
 HIS   0.004   0.001   HIS B  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.17 (17286)
  covalent geometry    : angle       0.52122 /  0.26 (23592)
  hydrogen bonds       : bond        0.04684 /  3.22 (  840)
  hydrogen bonds       : angle       4.15858 /  3.01 ( 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
  149 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.652 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.8000 (ptm160) cc_final: 0.7209 (ptm160)
REVERT: A  187 MET cc_start: 0.9259 (ptt) cc_final: 0.9059 (mpp)
REVERT: B  189 ASN cc_start: 0.8855 (m-40) cc_final: 0.8366 (t0)
REVERT: C  321 ARG cc_start: 0.8975 (mtp85) cc_final: 0.8768 (mtp85)
REVERT: D  126 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7247 (ptm160)
REVERT: E  189 ASN cc_start: 0.8849 (m-40) cc_final: 0.8344 (t0)
REVERT: F  321 ARG cc_start: 0.8976 (mtp85) cc_final: 0.8761 (mtp85)
  outliers start: 33
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1265
  time to fit residues: 28.0880
Evaluate side-chains
  132 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
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  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  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  112 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain F residue   53 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 142 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 102 optimal weight:   30.0000
   chunk 193 optimal weight:    3.9990
   chunk 196 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 147 optimal weight:    9.9990
   chunk 114 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.077873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.058574 restraints weight = 42314.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 3.41
r_work: 0.2665 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2670 r_free = 0.2670    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  17286  Z= 0.221
  Angle     :  0.561   8.175  23592  Z= 0.284
  Chirality :  0.040   0.133   2724
  Planarity :  0.004   0.037   2850
  Dihedral  : 10.052  60.032   2956
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.63 %
    Favored  : 85.93 %
  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:  1.35 (0.19), residues: 2020
  helix:  1.67 (0.15), residues: 1164
  sheet:  None (None), residues: 0
  loop : -0.12 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 321 
 TYR   0.017   0.002   TYR A 100 
 PHE   0.009   0.001   PHE B 282 
 TRP   0.008   0.001   TRP F 309 
 HIS   0.004   0.001   HIS B  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.22 (17286)
  covalent geometry    : angle       0.56143 /  0.28 (23592)
  hydrogen bonds       : bond        0.05057 /  3.47 (  840)
  hydrogen bonds       : angle       4.28498 /  3.10 ( 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
  152 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 110
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: B  189 ASN cc_start: 0.8854 (m-40) cc_final: 0.8359 (t0)
REVERT: C  321 ARG cc_start: 0.8969 (mtp85) cc_final: 0.8748 (mtp85)
REVERT: D   63 GLN cc_start: 0.7885 (tp40) cc_final: 0.7683 (tp-100)
REVERT: D  126 ARG cc_start: 0.8043 (ptm160) cc_final: 0.7192 (ptm160)
REVERT: E  189 ASN cc_start: 0.8860 (m-40) cc_final: 0.8367 (t0)
REVERT: F  321 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8743 (mtp85)
  outliers start: 42
  outliers final: 34
  residues processed: 145
  average time/residue: 0.1256
  time to fit residues: 28.6320
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  : 0.636 
-------------------------------------------------------------------------------
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  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  115 THR
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  115 THR
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  115 THR
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 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  112 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  178 HIS
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  115 THR
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:    2.9990
   chunk 166 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 135 optimal weight:    0.0870
   chunk 181 optimal weight:    4.9990
   chunk 112 optimal weight:   20.0000
   chunk 122 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 65 optimal weight:   50.0000
   chunk 204 optimal weight:   30.0000
   overall best weight:    3.6166

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.079559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.060361 restraints weight = 41344.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.40
r_work: 0.2714 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2722 r_free = 0.2722    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 = 0.2722 r_free = 0.2722    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.3029

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= 0.129
  Angle     :  0.507  10.402  23592  Z= 0.252
  Chirality :  0.037   0.132   2724
  Planarity :  0.003   0.037   2850
  Dihedral  :  9.980  60.042   2956
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.56 %
    Favored  : 85.58 %
  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:  1.61 (0.19), residues: 2020
  helix:  1.90 (0.15), residues: 1164
  sheet:  None (None), residues: 0
  loop : -0.03 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 321 
 TYR   0.011   0.001   TYR D 244 
 PHE   0.007   0.001   PHE D  90 
 TRP   0.011   0.001   TRP F 309 
 HIS   0.003   0.001   HIS E  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 (17286)
  covalent geometry    : angle       0.50712 /  0.25 (23592)
  hydrogen bonds       : bond        0.04203 /  2.89 (  840)
  hydrogen bonds       : angle       4.03141 /  2.91 ( 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
  149 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: B  189 ASN cc_start: 0.8870 (m-40) cc_final: 0.8332 (t0)
REVERT: C  321 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8709 (mtp85)
REVERT: D  126 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7281 (ptm160)
REVERT: D  186 GLN cc_start: 0.9415 (tt0) cc_final: 0.9036 (pp30)
REVERT: E  170 MET cc_start: 0.8616 (mmm) cc_final: 0.7916 (mmm)
REVERT: E  189 ASN cc_start: 0.8880 (m-40) cc_final: 0.8336 (t0)
REVERT: F  321 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8703 (mtp85)
  outliers start: 32
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1298
  time to fit residues: 29.2260
Evaluate side-chains
  134 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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 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  249 MET
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 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  249 MET
Chi-restraints excluded: chain F residue   53 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:    5.9990
   chunk 202 optimal weight:   20.0000
   chunk 61 optimal weight:    9.9990
   chunk 134 optimal weight:   20.0000
   chunk 80 optimal weight:   10.0000
   chunk 159 optimal weight:    7.9990
   chunk 114 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   chunk 138 optimal weight:    0.4980
   chunk 70 optimal weight:    8.9990
   chunk 74 optimal weight:   30.0000
   overall best weight:    4.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.079018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.059786 restraints weight = 41852.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 3.38
r_work: 0.2704 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2710
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2710 r_free = 0.2710    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2710 r_free = 0.2710    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2710
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.3075

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= 0.154
  Angle     :  0.530   9.329  23592  Z= 0.262
  Chirality :  0.038   0.132   2724
  Planarity :  0.003   0.036   2850
  Dihedral  :  9.976  60.047   2956
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.56 %
    Favored  : 85.41 %
  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:  1.58 (0.19), residues: 2020
  helix:  1.87 (0.15), residues: 1164
  sheet:  None (None), residues: 0
  loop : -0.03 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 321 
 TYR   0.012   0.001   TYR A 100 
 PHE   0.007   0.001   PHE D  90 
 TRP   0.008   0.001   TRP F 309 
 HIS   0.003   0.001   HIS E  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 (17286)
  covalent geometry    : angle       0.52975 /  0.26 (23592)
  hydrogen bonds       : bond        0.04362 /  3.00 (  840)
  hydrogen bonds       : angle       4.05864 /  2.93 ( 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
  147 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A   68 MET cc_start: 0.9214 (mtt) cc_final: 0.8878 (ptp)
REVERT: A  186 GLN cc_start: 0.9413 (tt0) cc_final: 0.9042 (pp30)
REVERT: B  189 ASN cc_start: 0.8847 (m-40) cc_final: 0.8324 (t0)
REVERT: C  321 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8704 (mmm-85)
REVERT: D  126 ARG cc_start: 0.8098 (ptm160) cc_final: 0.7305 (ptm160)
REVERT: D  186 GLN cc_start: 0.9400 (tt0) cc_final: 0.9116 (pp30)
REVERT: E  189 ASN cc_start: 0.8894 (m-40) cc_final: 0.8359 (t0)
REVERT: F  321 ARG cc_start: 0.8942 (mtp85) cc_final: 0.8704 (mtp85)
  outliers start: 35
  outliers final: 30
  residues processed: 141
  average time/residue: 0.1162
  time to fit residues: 25.5861
Evaluate side-chains
  140 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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 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 B residue  249 MET
Chi-restraints excluded: chain B residue  364 ILE
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  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  115 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain F residue   53 ILE
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  115 THR
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:   10.0000
   chunk 67 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0870
   chunk 90 optimal weight:    2.9990
   chunk 191 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 113 optimal weight:    9.9990
   overall best weight:    2.2164

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.080967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.061711 restraints weight = 41218.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 3.41
r_work: 0.2744 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
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 = 0.24   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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  17286  Z= 0.104
  Angle     :  0.513   8.714  23592  Z= 0.251
  Chirality :  0.037   0.133   2724
  Planarity :  0.003   0.033   2850
  Dihedral  :  9.938  60.038   2956
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.67 %
    Favored  : 85.58 %
  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   0.007   0.000   ARG E 321 
 TYR   0.011   0.001   TYR E 244 
 PHE   0.007   0.001   PHE D 222 
 TRP   0.011   0.001   TRP F 309 
 HIS   0.003   0.000   HIS D 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.10 (17286)
  covalent geometry    : angle       0.51268 /  0.25 (23592)
  hydrogen bonds       : bond        0.03770 /  2.59 (  840)
  hydrogen bonds       : angle       3.90371 /  2.82 ( 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
  151 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   68 MET cc_start: 0.9210 (mtt) cc_final: 0.8894 (ptp)
REVERT: A  186 GLN cc_start: 0.9370 (tt0) cc_final: 0.9057 (pp30)
REVERT: B  189 ASN cc_start: 0.8901 (m-40) cc_final: 0.8302 (t0)
REVERT: C  321 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8692 (mmm-85)
REVERT: D  126 ARG cc_start: 0.8104 (ptm160) cc_final: 0.7322 (ptm160)
REVERT: D  186 GLN cc_start: 0.9376 (tt0) cc_final: 0.8983 (pp30)
REVERT: E  170 MET cc_start: 0.8607 (mmm) cc_final: 0.8348 (mmt)
REVERT: E  189 ASN cc_start: 0.8908 (m-40) cc_final: 0.8305 (t0)
REVERT: F  321 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8691 (mmm-85)
  outliers start: 30
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1214
  time to fit residues: 27.2898
Evaluate side-chains
  136 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  138 SER
Chi-restraints excluded: chain B residue  249 MET
Chi-restraints excluded: chain C residue  113 VAL
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  138 SER
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 143 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:   50.0000
   chunk 135 optimal weight:   20.0000
   chunk 175 optimal weight:    0.1980
   chunk 196 optimal weight:    0.9990
   chunk 8 optimal weight:   30.0000
   overall best weight:    3.2386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.080407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.061198 restraints weight = 41376.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 3.41
r_work: 0.2733 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  17286  Z= 0.122
  Angle     :  0.525   8.719  23592  Z= 0.256
  Chirality :  0.037   0.133   2724
  Planarity :  0.003   0.032   2850
  Dihedral  :  9.921  60.040   2956
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 13.02 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.19), residues: 2020
  helix:  2.01 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop :  0.04 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 321 
 TYR   0.011   0.001   TYR D 244 
 PHE   0.008   0.001   PHE A 222 
 TRP   0.009   0.001   TRP C 309 
 HIS   0.003   0.001   HIS A 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 (17286)
  covalent geometry    : angle       0.52512 /  0.26 (23592)
  hydrogen bonds       : bond        0.03919 /  2.70 (  840)
  hydrogen bonds       : angle       3.92601 /  2.84 ( 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
  137 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  186 GLN cc_start: 0.9360 (tt0) cc_final: 0.8951 (pp30)
REVERT: B  189 ASN cc_start: 0.8874 (m-40) cc_final: 0.8271 (t0)
REVERT: D  126 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7313 (ptm160)
REVERT: D  186 GLN cc_start: 0.9366 (tt0) cc_final: 0.8952 (pp30)
REVERT: E  170 MET cc_start: 0.8609 (mmm) cc_final: 0.8367 (mmt)
REVERT: E  189 ASN cc_start: 0.8894 (m-40) cc_final: 0.8263 (t0)
  outliers start: 23
  outliers final: 22
  residues processed: 134
  average time/residue: 0.1149
  time to fit residues: 24.0836
Evaluate side-chains
  131 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
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  112 VAL
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  249 MET
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  249 MET
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  124 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 146 optimal weight:    7.9990
   chunk 114 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 168 optimal weight:   50.0000
   chunk 50 optimal weight:    5.9990
   chunk 138 optimal weight:   20.0000
   chunk 96 optimal weight:    0.1980
   chunk 158 optimal weight:    2.9990
   chunk 142 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    3.6388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.080287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.061012 restraints weight = 41133.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 3.41
r_work: 0.2730 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  17286  Z= 0.128
  Angle     :  0.531   9.339  23592  Z= 0.258
  Chirality :  0.037   0.134   2724
  Planarity :  0.003   0.032   2850
  Dihedral  :  9.909  60.029   2956
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.08 %
    Favored  : 85.41 %
  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:  1.75 (0.19), residues: 2020
  helix:  2.00 (0.15), residues: 1162
  sheet:  None (None), residues: 0
  loop :  0.04 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 321 
 TYR   0.011   0.001   TYR D 244 
 PHE   0.007   0.001   PHE A 222 
 TRP   0.009   0.001   TRP F 309 
 HIS   0.003   0.001   HIS D 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 (17286)
  covalent geometry    : angle       0.53080 /  0.26 (23592)
  hydrogen bonds       : bond        0.03963 /  2.72 (  840)
  hydrogen bonds       : angle       3.93310 /  2.85 ( 2322)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2879.80 seconds
wall clock time: 50 minutes 28.38 seconds (3028.38 seconds total)