Starting phenix.real_space_refine
on Sun Oct 13 12:15:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/10_2024/8iuo_35728.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/10_2024/8iuo_35728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/10_2024/8iuo_35728.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/10_2024/8iuo_35728.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/10_2024/8iuo_35728.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/10_2024/8iuo_35728.cif"
  }
  resolution = 3.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.024
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      35      5.49       5
     S      85      5.16       5
     C    9225      2.51       5
     N    2530      2.21       5
     O    2910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 14785
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2817
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 8, 'TRANS': 353}
    Chain: "A"
      Number of atoms: 2817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2817
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 8, 'TRANS': 353}
    Chain: "F"
      Number of atoms: 700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 700
          Classifications: {'RNA': 35}
          Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 5, 'rna3p': 29}
    Chain: "B"
      Number of atoms: 2817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2817
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 8, 'TRANS': 353}
    Chain: "D"
      Number of atoms: 2817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2817
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 8, 'TRANS': 353}
    Chain: "E"
      Number of atoms: 2817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2817
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 8, 'TRANS': 353}
  Time building chain proxies: 10.13, per 1000 atoms: 0.69
  Number of scatterers: 14785
  At special positions: 0
  Unit cell: (171.7, 147.05, 121.55, 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      85     16.00
     P      35     15.00
     O    2910      8.00
     N    2530      7.00
     C    9225      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: 4.01
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3310

  Finding SS restraints...
    Secondary structure from input PDB file:
      110 helices and 10 sheets defined
      71.5% alpha, 5.0% beta
      0 base pairs and 20 stacking pairs defined.
    Time for finding SS restraints: 4.88
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1 through 6
      removed outlier: 3.628A  pdb=" N   LYS C   5 " --> pdb=" O   ALA C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 20
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 40 through 54
    Processing helix  chain 'C' and resid 61 through 75
    Processing helix  chain 'C' and resid 75 through 87
    Processing helix  chain 'C' and resid 120 through 140
    Processing helix  chain 'C' and resid 146 through 150
      removed outlier: 3.719A  pdb=" N   ARG C 150 " --> pdb=" O   PRO C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 171
      removed outlier: 3.711A  pdb=" N   ILE C 163 " --> pdb=" O   ILE C 159 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LYS C 170 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 189
    Processing helix  chain 'C' and resid 190 through 197
    Processing helix  chain 'C' and resid 201 through 216
    Processing helix  chain 'C' and resid 217 through 233
      removed outlier: 3.961A  pdb=" N   ASP C 221 " --> pdb=" O   PRO C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 250
      removed outlier: 3.610A  pdb=" N   ALA C 250 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 268
      removed outlier: 3.947A  pdb=" N   ARG C 259 " --> pdb=" O   GLN C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 273
    Processing helix  chain 'C' and resid 274 through 279
    Processing helix  chain 'C' and resid 280 through 295
    Processing helix  chain 'C' and resid 306 through 312
      removed outlier: 3.836A  pdb=" N   SER C 310 " --> pdb=" O   PRO C 307 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 311 " --> pdb=" O   LYS C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 316
      removed outlier: 4.003A  pdb=" N   GLN C 316 " --> pdb=" O   SER C 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 313 through 316'
    Processing helix  chain 'C' and resid 317 through 331
    Processing helix  chain 'C' and resid 343 through 360
      removed outlier: 3.776A  pdb=" N   ASN C 360 " --> pdb=" O   GLN C 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1 through 6
      removed outlier: 3.628A  pdb=" N   LYS A   5 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 20
    Processing helix  chain 'A' and resid 37 through 39
      No H-bonds generated for 'chain 'A' and resid 37 through 39'
    Processing helix  chain 'A' and resid 40 through 54
    Processing helix  chain 'A' and resid 61 through 75
    Processing helix  chain 'A' and resid 75 through 87
    Processing helix  chain 'A' and resid 120 through 140
    Processing helix  chain 'A' and resid 146 through 150
      removed outlier: 3.720A  pdb=" N   ARG A 150 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 171
      removed outlier: 3.711A  pdb=" N   ILE A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 189
    Processing helix  chain 'A' and resid 190 through 197
    Processing helix  chain 'A' and resid 201 through 216
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.962A  pdb=" N   ASP A 221 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 250
      removed outlier: 3.611A  pdb=" N   ALA A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.946A  pdb=" N   ARG A 259 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
    Processing helix  chain 'A' and resid 274 through 279
    Processing helix  chain 'A' and resid 280 through 295
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.836A  pdb=" N   SER A 310 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 311 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 4.003A  pdb=" N   GLN A 316 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 343 through 360
      removed outlier: 3.776A  pdb=" N   ASN A 360 " --> pdb=" O   GLN A 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 6
      removed outlier: 3.628A  pdb=" N   LYS B   5 " --> pdb=" O   ALA B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 20
    Processing helix  chain 'B' and resid 37 through 39
      No H-bonds generated for 'chain 'B' and resid 37 through 39'
    Processing helix  chain 'B' and resid 40 through 54
    Processing helix  chain 'B' and resid 61 through 75
    Processing helix  chain 'B' and resid 75 through 87
    Processing helix  chain 'B' and resid 120 through 140
    Processing helix  chain 'B' and resid 146 through 150
      removed outlier: 3.719A  pdb=" N   ARG B 150 " --> pdb=" O   PRO B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 171
      removed outlier: 3.712A  pdb=" N   ILE B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 189
    Processing helix  chain 'B' and resid 190 through 197
    Processing helix  chain 'B' and resid 201 through 216
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.962A  pdb=" N   ASP B 221 " --> pdb=" O   PRO B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 250
      removed outlier: 3.610A  pdb=" N   ALA B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 268
      removed outlier: 3.947A  pdb=" N   ARG B 259 " --> pdb=" O   GLN B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 273
    Processing helix  chain 'B' and resid 274 through 279
    Processing helix  chain 'B' and resid 280 through 295
    Processing helix  chain 'B' and resid 306 through 312
      removed outlier: 3.836A  pdb=" N   SER B 310 " --> pdb=" O   PRO B 307 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU B 311 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 316
      removed outlier: 4.004A  pdb=" N   GLN B 316 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 313 through 316'
    Processing helix  chain 'B' and resid 317 through 331
    Processing helix  chain 'B' and resid 343 through 360
      removed outlier: 3.776A  pdb=" N   ASN B 360 " --> pdb=" O   GLN B 356 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1 through 6
      removed outlier: 3.628A  pdb=" N   LYS D   5 " --> pdb=" O   ALA D   2 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 20
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 40 through 54
    Processing helix  chain 'D' and resid 61 through 75
    Processing helix  chain 'D' and resid 75 through 87
    Processing helix  chain 'D' and resid 120 through 140
    Processing helix  chain 'D' and resid 146 through 150
      removed outlier: 3.719A  pdb=" N   ARG D 150 " --> pdb=" O   PRO D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 171
      removed outlier: 3.711A  pdb=" N   ILE D 163 " --> pdb=" O   ILE D 159 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS D 170 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 189
    Processing helix  chain 'D' and resid 190 through 197
    Processing helix  chain 'D' and resid 201 through 216
    Processing helix  chain 'D' and resid 217 through 233
      removed outlier: 3.962A  pdb=" N   ASP D 221 " --> pdb=" O   PRO D 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 250
      removed outlier: 3.610A  pdb=" N   ALA D 250 " --> pdb=" O   LEU D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 268
      removed outlier: 3.947A  pdb=" N   ARG D 259 " --> pdb=" O   GLN D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 273
    Processing helix  chain 'D' and resid 274 through 279
    Processing helix  chain 'D' and resid 280 through 295
    Processing helix  chain 'D' and resid 306 through 312
      removed outlier: 3.836A  pdb=" N   SER D 310 " --> pdb=" O   PRO D 307 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU D 311 " --> pdb=" O   LYS D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 313 through 316
      removed outlier: 4.003A  pdb=" N   GLN D 316 " --> pdb=" O   SER D 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 313 through 316'
    Processing helix  chain 'D' and resid 317 through 331
    Processing helix  chain 'D' and resid 343 through 360
      removed outlier: 3.777A  pdb=" N   ASN D 360 " --> pdb=" O   GLN D 356 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1 through 6
      removed outlier: 3.628A  pdb=" N   LYS E   5 " --> pdb=" O   ALA E   2 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 9 through 20
    Processing helix  chain 'E' and resid 37 through 39
      No H-bonds generated for 'chain 'E' and resid 37 through 39'
    Processing helix  chain 'E' and resid 40 through 54
    Processing helix  chain 'E' and resid 61 through 75
    Processing helix  chain 'E' and resid 75 through 87
    Processing helix  chain 'E' and resid 120 through 140
    Processing helix  chain 'E' and resid 146 through 150
      removed outlier: 3.719A  pdb=" N   ARG E 150 " --> pdb=" O   PRO E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 155 through 171
      removed outlier: 3.712A  pdb=" N   ILE E 163 " --> pdb=" O   ILE E 159 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS E 170 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 189
    Processing helix  chain 'E' and resid 190 through 197
    Processing helix  chain 'E' and resid 201 through 216
    Processing helix  chain 'E' and resid 217 through 233
      removed outlier: 3.961A  pdb=" N   ASP E 221 " --> pdb=" O   PRO E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 237 through 250
      removed outlier: 3.610A  pdb=" N   ALA E 250 " --> pdb=" O   LEU E 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 255 through 268
      removed outlier: 3.946A  pdb=" N   ARG E 259 " --> pdb=" O   GLN E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 273
    Processing helix  chain 'E' and resid 274 through 279
    Processing helix  chain 'E' and resid 280 through 295
    Processing helix  chain 'E' and resid 306 through 312
      removed outlier: 3.836A  pdb=" N   SER E 310 " --> pdb=" O   PRO E 307 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU E 311 " --> pdb=" O   LYS E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 313 through 316
      removed outlier: 4.004A  pdb=" N   GLN E 316 " --> pdb=" O   SER E 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 313 through 316'
    Processing helix  chain 'E' and resid 317 through 331
    Processing helix  chain 'E' and resid 343 through 360
      removed outlier: 3.777A  pdb=" N   ASN E 360 " --> pdb=" O   GLN E 356 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 35
    Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 104
      removed outlier: 4.196A  pdb=" N   ASP C  96 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35
    Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 104
      removed outlier: 4.195A  pdb=" N   ASP A  96 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35
    Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 104
      removed outlier: 4.195A  pdb=" N   ASP B  96 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 35
    Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 104
      removed outlier: 4.197A  pdb=" N   ASP D  96 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 35
    Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 104
      removed outlier: 4.196A  pdb=" N   ASP E  96 " --> pdb=" O   THR E 115 " (cutoff:3.500A)

    880 hydrogen bonds defined for protein.
    2520 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      20 stacking parallelities
  Total time for adding SS restraints: 4.63

  Time building geometry restraints manager: 4.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4620
        1.34 -     1.45: 2287
        1.45 -     1.57: 7958
        1.57 -     1.69: 69
        1.69 -     1.81: 155
  Bond restraints: 15089
  Sorted by residual:
  bond pdb=" N   GLY E 236 "
       pdb=" CA  GLY E 236 "
    ideal  model  delta    sigma   weight residual
    1.443  1.478 -0.035 1.17e-02 7.31e+03 8.81e+00
  bond pdb=" N   VAL E 239 "
       pdb=" CA  VAL E 239 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.68e+00
  bond pdb=" N   VAL C 239 "
       pdb=" CA  VAL C 239 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.31e+00
  bond pdb=" N   SER D 237 "
       pdb=" CA  SER D 237 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.034 1.17e-02 7.31e+03 8.23e+00
  bond pdb=" N   VAL B 239 "
       pdb=" CA  VAL B 239 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 1.14e-02 7.69e+03 8.22e+00
  ... (remaining 15084 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 19055
        1.31 -     2.63: 1174
        2.63 -     3.94: 159
        3.94 -     5.25: 56
        5.25 -     6.56: 17
  Bond angle restraints: 20461
  Sorted by residual:
  angle pdb=" CA  GLY A 236 "
        pdb=" C   GLY A 236 "
        pdb=" O   GLY A 236 "
      ideal   model   delta    sigma   weight residual
     122.16  118.07    4.09 8.20e-01 1.49e+00 2.48e+01
  angle pdb=" N   ASN C 187 "
        pdb=" CA  ASN C 187 "
        pdb=" C   ASN C 187 "
      ideal   model   delta    sigma   weight residual
     113.50  108.24    5.26 1.23e+00 6.61e-01 1.83e+01
  angle pdb=" N   ARG A 234 "
        pdb=" CA  ARG A 234 "
        pdb=" C   ARG A 234 "
      ideal   model   delta    sigma   weight residual
     113.61  107.83    5.78 1.50e+00 4.44e-01 1.48e+01
  angle pdb=" O3'   U F1014 "
        pdb=" C3'   U F1014 "
        pdb=" C2'   U F1014 "
      ideal   model   delta    sigma   weight residual
     113.70  118.87   -5.17 1.50e+00 4.44e-01 1.19e+01
  angle pdb=" C   ILE D 104 "
        pdb=" N   ASN D 105 "
        pdb=" CA  ASN D 105 "
      ideal   model   delta    sigma   weight residual
     121.54  128.10   -6.56 1.91e+00 2.74e-01 1.18e+01
  ... (remaining 20456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 8937
       34.98 -    69.96: 266
       69.96 -   104.94: 15
      104.94 -   139.92: 3
      139.92 -   174.89: 1
  Dihedral angle restraints: 9222
    sinusoidal: 4032
      harmonic: 5190
  Sorted by residual:
  dihedral pdb=" C4'   U F1028 "
           pdb=" C3'   U F1028 "
           pdb=" O3'   U F1028 "
           pdb=" P     U F1029 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.11  174.89     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  SER E 153 "
           pdb=" C   SER E 153 "
           pdb=" N   PRO E 154 "
           pdb=" CA  PRO E 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.99  -18.01     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  SER C 153 "
           pdb=" C   SER C 153 "
           pdb=" N   PRO C 154 "
           pdb=" CA  PRO C 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 9219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1790
       0.047 -    0.094: 457
       0.094 -    0.141: 75
       0.141 -    0.189: 9
       0.189 -    0.236: 4
  Chirality restraints: 2335
  Sorted by residual:
  chirality pdb=" C3'   U F1021 "
            pdb=" C4'   U F1021 "
            pdb=" O3'   U F1021 "
            pdb=" C2'   U F1021 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.24   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" C3'   U F1007 "
            pdb=" C4'   U F1007 "
            pdb=" O3'   U F1007 "
            pdb=" C2'   U F1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.24   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C3'   U F1014 "
            pdb=" C4'   U F1014 "
            pdb=" O3'   U F1014 "
            pdb=" C2'   U F1014 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.24   -0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 2332 not shown)

  Planarity restraints: 2510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 215 "   -0.014 2.00e-02 2.50e+03   2.79e-02 7.78e+00
        pdb=" C   LYS C 215 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LYS C 215 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   HIS C 216 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 215 "   -0.012 2.00e-02 2.50e+03   2.52e-02 6.35e+00
        pdb=" C   LYS B 215 "    0.044 2.00e-02 2.50e+03
        pdb=" O   LYS B 215 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   HIS B 216 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 215 "   -0.012 2.00e-02 2.50e+03   2.45e-02 5.99e+00
        pdb=" C   LYS A 215 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LYS A 215 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   HIS A 216 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2507 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 387
        2.69 -     3.24: 16470
        3.24 -     3.80: 24264
        3.80 -     4.35: 28856
        4.35 -     4.90: 47479
  Nonbonded interactions: 117456
  Sorted by model distance:
  nonbonded pdb=" O2'   U F1028 "
            pdb=" OP1   U F1029 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OP2   U F1008 "
            pdb=" ND2 ASN E 188 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OP2   U F1029 "
            pdb=" ND2 ASN D 188 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OP2   U F1022 "
            pdb=" ND2 ASN B 188 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" NH1 ARG A 184 "
            pdb=" OP1   U F1035 "
     model   vdw
     2.239 3.120
  ... (remaining 117451 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             3.750
  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:          0.630
  Check model and map are aligned:         0.130
  Set scattering table:                    0.150
  Process input model:                     38.760
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.070
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052  15089  Z= 0.492
  Angle     :  0.738   6.563  20461  Z= 0.443
  Chirality :  0.043   0.236   2335
  Planarity :  0.004   0.046   2510
  Dihedral  : 16.368 174.894   5912
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  2.79 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.18), residues: 1800
  helix: -0.79 (0.13), residues: 1165
  sheet: -3.72 (0.41), residues: 125
  loop : -2.70 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D 260 
 HIS   0.004   0.001   HIS D 218 
 PHE   0.011   0.001   PHE A 247 
 TYR   0.010   0.001   TYR C 210 
 ARG   0.024   0.001   ARG E  27 

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 1.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 MET cc_start: 0.7972 (ptp) cc_final: 0.7409 (ptm)
REVERT: C  271 MET cc_start: 0.9268 (mmm) cc_final: 0.8521 (mtp)
REVERT: C  315 THR cc_start: 0.8675 (m) cc_final: 0.8434 (m)
REVERT: A  194 MET cc_start: 0.7853 (mtm) cc_final: 0.7582 (mtt)
REVERT: B  158 MET cc_start: 0.8021 (mmm) cc_final: 0.7776 (mmm)
REVERT: B  286 GLU cc_start: 0.7953 (tp30) cc_final: 0.7261 (tp30)
REVERT: B  297 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6846 (tm-30)
REVERT: B  305 ASN cc_start: 0.7947 (m-40) cc_final: 0.7445 (p0)
REVERT: D   50 MET cc_start: 0.8635 (mtt) cc_final: 0.8327 (mtm)
REVERT: D   71 MET cc_start: 0.8935 (mtm) cc_final: 0.8705 (mtt)
REVERT: D  142 MET cc_start: 0.8464 (ptp) cc_final: 0.7780 (ptp)
REVERT: D  263 LEU cc_start: 0.8843 (tp) cc_final: 0.8578 (tt)
REVERT: E  134 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7402 (m)
REVERT: E  216 HIS cc_start: 0.5384 (OUTLIER) cc_final: 0.5087 (m-70)
  outliers start: 33
  outliers final: 9
  residues processed: 234
  average time/residue: 0.3861
  time to fit residues: 125.5031
Evaluate side-chains
  125 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  216 HIS
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue  216 HIS
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  216 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 154 optimal weight:    7.9990
   chunk 138 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 93 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 143 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 166 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  13 ASN
** A  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  59 HIS
A 249 ASN
B  58 ASN
B 216 HIS
D  13 ASN
D  16 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 ASN
E 230 GLN
E 249 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  15089  Z= 0.323
  Angle     :  0.685   9.991  20461  Z= 0.361
  Chirality :  0.044   0.254   2335
  Planarity :  0.004   0.035   2510
  Dihedral  : 11.726 155.720   2533
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.10 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.20), residues: 1800
  helix:  0.83 (0.15), residues: 1170
  sheet: -3.15 (0.38), residues: 125
  loop : -2.46 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 260 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.014   0.002   PHE D 111 
 TYR   0.020   0.002   TYR C  88 
 ARG   0.007   0.001   ARG D 101 

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 2.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    9 ASN cc_start: 0.8676 (t0) cc_final: 0.8425 (t0)
REVERT: C   50 MET cc_start: 0.8960 (mtp) cc_final: 0.8679 (mtp)
REVERT: C  105 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.5864 (p0)
REVERT: C  271 MET cc_start: 0.9318 (mmm) cc_final: 0.8557 (mtp)
REVERT: C  313 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8270 (p)
REVERT: A  109 MET cc_start: 0.6585 (mmt) cc_final: 0.6234 (mmt)
REVERT: A  194 MET cc_start: 0.8106 (mtm) cc_final: 0.7849 (mtt)
REVERT: B   50 MET cc_start: 0.9085 (mtp) cc_final: 0.8535 (ttm)
REVERT: B   71 MET cc_start: 0.9262 (mtm) cc_final: 0.8885 (mtm)
REVERT: B  271 MET cc_start: 0.8581 (mtp) cc_final: 0.8260 (mtp)
REVERT: B  297 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7339 (tm-30)
REVERT: B  305 ASN cc_start: 0.8425 (m-40) cc_final: 0.7679 (p0)
REVERT: D   50 MET cc_start: 0.8815 (mtt) cc_final: 0.8492 (mtp)
REVERT: D   67 MET cc_start: 0.9399 (mmm) cc_final: 0.8748 (mmm)
REVERT: D   71 MET cc_start: 0.9101 (mtm) cc_final: 0.8494 (mtm)
REVERT: D  158 MET cc_start: 0.8774 (mmt) cc_final: 0.7909 (mmt)
REVERT: D  162 CYS cc_start: 0.9263 (m) cc_final: 0.8830 (m)
REVERT: E  138 MET cc_start: 0.9284 (mmm) cc_final: 0.9077 (mmm)
REVERT: E  282 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: E  297 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7154 (tm-30)
  outliers start: 27
  outliers final: 11
  residues processed: 149
  average time/residue: 0.3771
  time to fit residues: 81.0942
Evaluate side-chains
  114 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  313 SER
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  362 VAL
Chi-restraints excluded: chain E residue   27 ARG
Chi-restraints excluded: chain E residue  141 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 92 optimal weight:    0.0470
   chunk 51 optimal weight:    5.9990
   chunk 138 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 166 optimal weight:    0.7980
   chunk 179 optimal weight:    5.9990
   chunk 148 optimal weight:    0.9990
   chunk 165 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 133 optimal weight:    0.8980
   overall best weight:    1.5482

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

Flipped N/Q/H residues before XYZ refinement:
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 230 GLN
A   9 ASN
** A  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  16 GLN
D  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  15089  Z= 0.157
  Angle     :  0.543   8.486  20461  Z= 0.284
  Chirality :  0.039   0.248   2335
  Planarity :  0.003   0.032   2510
  Dihedral  : 11.499 160.578   2518
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.56 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.20), residues: 1800
  helix:  1.23 (0.15), residues: 1205
  sheet: -1.63 (0.53), residues: 70
  loop : -2.66 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 260 
 HIS   0.003   0.001   HIS C 100 
 PHE   0.011   0.001   PHE A 111 
 TYR   0.009   0.001   TYR D  23 
 ARG   0.004   0.000   ARG B 101 

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 2.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    9 ASN cc_start: 0.8659 (t0) cc_final: 0.8186 (t0)
REVERT: C   50 MET cc_start: 0.8911 (mtp) cc_final: 0.8586 (mtp)
REVERT: C  105 ASN cc_start: 0.6331 (OUTLIER) cc_final: 0.5908 (p0)
REVERT: A  194 MET cc_start: 0.8067 (mtm) cc_final: 0.7794 (mtt)
REVERT: A  281 MET cc_start: 0.7972 (mmm) cc_final: 0.7585 (tpt)
REVERT: B   71 MET cc_start: 0.9190 (mtm) cc_final: 0.8872 (mtm)
REVERT: B  162 CYS cc_start: 0.9129 (m) cc_final: 0.8801 (m)
REVERT: B  271 MET cc_start: 0.8440 (mtp) cc_final: 0.7892 (mtp)
REVERT: B  297 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: B  305 ASN cc_start: 0.8510 (m-40) cc_final: 0.7741 (p0)
REVERT: D   50 MET cc_start: 0.8782 (mtt) cc_final: 0.8512 (mtp)
REVERT: D   67 MET cc_start: 0.9365 (mmm) cc_final: 0.8659 (mmm)
REVERT: D   71 MET cc_start: 0.9021 (mtm) cc_final: 0.8480 (mtm)
REVERT: D  142 MET cc_start: 0.8221 (ptp) cc_final: 0.7978 (ptt)
REVERT: D  158 MET cc_start: 0.8684 (mmt) cc_final: 0.7804 (mmt)
REVERT: D  162 CYS cc_start: 0.9206 (m) cc_final: 0.8820 (m)
REVERT: E  282 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: E  297 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7212 (tm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 137
  average time/residue: 0.3039
  time to fit residues: 62.6107
Evaluate side-chains
  117 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 2.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   48 CYS
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain D residue   16 GLN
Chi-restraints excluded: chain D residue  141 GLU
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain E residue   27 ARG
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue  141 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 164 optimal weight:    4.9990
   chunk 125 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   chunk 167 optimal weight:    6.9990
   chunk 176 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 158 optimal weight:    0.4980
   chunk 47 optimal weight:   10.0000
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
C 124 GLN
** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  15089  Z= 0.242
  Angle     :  0.581  10.042  20461  Z= 0.304
  Chirality :  0.040   0.260   2335
  Planarity :  0.003   0.032   2510
  Dihedral  : 11.379 159.301   2517
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.62 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.20), residues: 1800
  helix:  1.41 (0.15), residues: 1170
  sheet: -1.01 (0.56), residues: 70
  loop : -2.33 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 260 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.027   0.001   PHE B 223 
 TYR   0.012   0.001   TYR E 347 
 ARG   0.006   0.000   ARG B 101 

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 1.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    9 ASN cc_start: 0.8654 (t0) cc_final: 0.8413 (t0)
REVERT: C   50 MET cc_start: 0.8957 (mtp) cc_final: 0.8639 (mtp)
REVERT: C  105 ASN cc_start: 0.6502 (OUTLIER) cc_final: 0.6149 (p0)
REVERT: C  162 CYS cc_start: 0.9087 (m) cc_final: 0.8568 (t)
REVERT: A  194 MET cc_start: 0.8111 (mtm) cc_final: 0.7809 (mtt)
REVERT: A  281 MET cc_start: 0.7952 (mmm) cc_final: 0.7685 (tpt)
REVERT: B   71 MET cc_start: 0.9258 (mtm) cc_final: 0.8950 (mtm)
REVERT: B  162 CYS cc_start: 0.9153 (m) cc_final: 0.8749 (m)
REVERT: B  297 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7411 (tm-30)
REVERT: B  305 ASN cc_start: 0.8721 (m-40) cc_final: 0.7825 (p0)
REVERT: D   50 MET cc_start: 0.8791 (mtt) cc_final: 0.8538 (mtp)
REVERT: D   67 MET cc_start: 0.9389 (mmm) cc_final: 0.8740 (mmm)
REVERT: D   71 MET cc_start: 0.9052 (mtm) cc_final: 0.8504 (mtm)
REVERT: D  158 MET cc_start: 0.8747 (mmt) cc_final: 0.8052 (mmp)
REVERT: D  162 CYS cc_start: 0.9243 (m) cc_final: 0.8828 (m)
REVERT: E  297 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7311 (tm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2575
  time to fit residues: 48.3251
Evaluate side-chains
  111 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain D residue  141 GLU
Chi-restraints excluded: chain E residue   27 ARG
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue  141 GLU
Chi-restraints excluded: chain E residue  177 SER
Chi-restraints excluded: chain E residue  239 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 131 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 150 optimal weight:    9.9990
   chunk 122 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 158 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   overall best weight:    5.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: