Starting phenix.real_space_refine
on Wed Nov 19 09:33:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ach_9592/11_2025/6ach_9592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ach_9592/11_2025/6ach_9592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ach_9592/11_2025/6ach_9592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ach_9592/11_2025/6ach_9592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ach_9592/11_2025/6ach_9592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ach_9592/11_2025/6ach_9592.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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      16      5.49       5
     S     136      5.16       5
     C   14536      2.51       5
     N    4136      2.21       5
     O    4416      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23240
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2861
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 364, 2829
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 11, 'TRANS': 352}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 364, 2829
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 11, 'TRANS': 352}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2841
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, F, G, H
  Time building chain proxies: 3.76, per 1000 atoms: 0.16
  Number of scatterers: 23240
  At special positions: 0
  Unit cell: (126.896, 126.896, 119.504, 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     136     16.00
     P      16     15.00
     O    4416      8.00
     N    4136      7.00
     C   14536      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: 1.88
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5344

  Finding SS restraints...
    Secondary structure from input PDB file:
      112 helices and 12 sheets defined
      48.6% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR A  10 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
      removed outlier: 4.254A  pdb=" N   PHE A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 166
    Processing helix  chain 'A' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 217
    Processing helix  chain 'A' and resid 247 through 251
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.771A  pdb=" N   GLY A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
    Processing helix  chain 'A' and resid 297 through 300
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 312 through 328
    Processing helix  chain 'A' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP A 336 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG A 350 " --> pdb=" O   MET A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR B  10 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA B  54 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 105
      removed outlier: 4.253A  pdb=" N   PHE B  96 " --> pdb=" O   ASN B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 166
    Processing helix  chain 'B' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU B 188 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 217
    Processing helix  chain 'B' and resid 247 through 251
    Processing helix  chain 'B' and resid 266 through 277
      removed outlier: 3.770A  pdb=" N   GLY B 270 " --> pdb=" O   GLU B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE B 286 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
    Processing helix  chain 'B' and resid 297 through 300
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 312 through 328
    Processing helix  chain 'B' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP B 336 " --> pdb=" O   TYR B 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG B 350 " --> pdb=" O   MET B 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR C  10 " --> pdb=" O   TYR C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA C  54 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 105
      removed outlier: 4.254A  pdb=" N   PHE C  96 " --> pdb=" O   ASN C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 166
    Processing helix  chain 'C' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU C 188 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 217
    Processing helix  chain 'C' and resid 247 through 251
    Processing helix  chain 'C' and resid 266 through 277
      removed outlier: 3.770A  pdb=" N   GLY C 270 " --> pdb=" O   GLU C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE C 286 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
    Processing helix  chain 'C' and resid 297 through 300
    Processing helix  chain 'C' and resid 302 through 311
    Processing helix  chain 'C' and resid 312 through 328
    Processing helix  chain 'C' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP C 336 " --> pdb=" O   TYR C 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG C 350 " --> pdb=" O   MET C 346 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR D  10 " --> pdb=" O   TYR D   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA D  54 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 105
      removed outlier: 4.253A  pdb=" N   PHE D  96 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 166
    Processing helix  chain 'D' and resid 184 through 196
      removed outlier: 3.589A  pdb=" N   LEU D 188 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 217
    Processing helix  chain 'D' and resid 247 through 251
    Processing helix  chain 'D' and resid 266 through 277
      removed outlier: 3.770A  pdb=" N   GLY D 270 " --> pdb=" O   GLU D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE D 286 " --> pdb=" O   PRO D 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 296
    Processing helix  chain 'D' and resid 297 through 300
    Processing helix  chain 'D' and resid 302 through 311
    Processing helix  chain 'D' and resid 312 through 328
    Processing helix  chain 'D' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP D 336 " --> pdb=" O   TYR D 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG D 350 " --> pdb=" O   MET D 346 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR E  10 " --> pdb=" O   TYR E   6 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA E  54 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 105
      removed outlier: 4.254A  pdb=" N   PHE E  96 " --> pdb=" O   ASN E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 146 through 166
    Processing helix  chain 'E' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU E 188 " --> pdb=" O   VAL E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 206 through 217
    Processing helix  chain 'E' and resid 247 through 251
    Processing helix  chain 'E' and resid 266 through 277
      removed outlier: 3.771A  pdb=" N   GLY E 270 " --> pdb=" O   GLU E 266 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE E 286 " --> pdb=" O   PRO E 282 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 288 through 296
    Processing helix  chain 'E' and resid 297 through 300
    Processing helix  chain 'E' and resid 302 through 311
    Processing helix  chain 'E' and resid 312 through 328
    Processing helix  chain 'E' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP E 336 " --> pdb=" O   TYR E 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG E 350 " --> pdb=" O   MET E 346 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR F  10 " --> pdb=" O   TYR F   6 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA F  54 " --> pdb=" O   SER F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 105
      removed outlier: 4.254A  pdb=" N   PHE F  96 " --> pdb=" O   ASN F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 146 through 166
    Processing helix  chain 'F' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU F 188 " --> pdb=" O   VAL F 184 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 206 through 217
    Processing helix  chain 'F' and resid 247 through 251
    Processing helix  chain 'F' and resid 266 through 277
      removed outlier: 3.770A  pdb=" N   GLY F 270 " --> pdb=" O   GLU F 266 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE F 286 " --> pdb=" O   PRO F 282 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 288 through 296
    Processing helix  chain 'F' and resid 297 through 300
    Processing helix  chain 'F' and resid 302 through 311
    Processing helix  chain 'F' and resid 312 through 328
    Processing helix  chain 'F' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP F 336 " --> pdb=" O   TYR F 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG F 350 " --> pdb=" O   MET F 346 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR G  10 " --> pdb=" O   TYR G   6 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA G  54 " --> pdb=" O   SER G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 105
      removed outlier: 4.254A  pdb=" N   PHE G  96 " --> pdb=" O   ASN G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 146 through 166
    Processing helix  chain 'G' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU G 188 " --> pdb=" O   VAL G 184 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 206 through 217
    Processing helix  chain 'G' and resid 247 through 251
    Processing helix  chain 'G' and resid 266 through 277
      removed outlier: 3.771A  pdb=" N   GLY G 270 " --> pdb=" O   GLU G 266 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE G 286 " --> pdb=" O   PRO G 282 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 288 through 296
    Processing helix  chain 'G' and resid 297 through 300
    Processing helix  chain 'G' and resid 302 through 311
    Processing helix  chain 'G' and resid 312 through 328
    Processing helix  chain 'G' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP G 336 " --> pdb=" O   TYR G 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG G 350 " --> pdb=" O   MET G 346 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 11
      removed outlier: 3.864A  pdb=" N   TYR H  10 " --> pdb=" O   TYR H   6 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 50 through 72
      removed outlier: 4.061A  pdb=" N   ALA H  54 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 92 through 105
      removed outlier: 4.254A  pdb=" N   PHE H  96 " --> pdb=" O   ASN H  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 146 through 166
    Processing helix  chain 'H' and resid 184 through 196
      removed outlier: 3.588A  pdb=" N   LEU H 188 " --> pdb=" O   VAL H 184 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 206 through 217
    Processing helix  chain 'H' and resid 247 through 251
    Processing helix  chain 'H' and resid 266 through 277
      removed outlier: 3.770A  pdb=" N   GLY H 270 " --> pdb=" O   GLU H 266 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 282 through 287
      removed outlier: 3.682A  pdb=" N   ILE H 286 " --> pdb=" O   PRO H 282 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 288 through 296
    Processing helix  chain 'H' and resid 297 through 300
    Processing helix  chain 'H' and resid 302 through 311
    Processing helix  chain 'H' and resid 312 through 328
    Processing helix  chain 'H' and resid 330 through 350
      removed outlier: 3.970A  pdb=" N   ASP H 336 " --> pdb=" O   TYR H 332 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG H 350 " --> pdb=" O   MET H 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114
      removed outlier: 5.940A  pdb=" N   LEU A  40 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR A  81 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY A  42 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE A  83 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG A  44 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY A  78 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS A  26 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS B  26 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY B  78 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU B  40 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR B  81 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY B  42 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE B  83 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG B  44 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL A 175 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA A 235 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA A 177 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL B 175 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA B 235 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA B 177 " --> pdb=" O   ALA B 235 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 110 through 114
      removed outlier: 5.940A  pdb=" N   LEU C  40 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR C  81 " --> pdb=" O   LEU C  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY C  42 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE C  83 " --> pdb=" O   GLY C  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG C  44 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY C  78 " --> pdb=" O   HIS C  32 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS C  26 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS D  26 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY D  78 " --> pdb=" O   HIS D  32 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU D  40 " --> pdb=" O   GLY D  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR D  81 " --> pdb=" O   LEU D  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY D  42 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE D  83 " --> pdb=" O   GLY D  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG D  44 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL C 175 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA C 235 " --> pdb=" O   VAL C 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA C 177 " --> pdb=" O   ALA C 235 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL D 175 " --> pdb=" O   ILE D 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA D 235 " --> pdb=" O   VAL D 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA D 177 " --> pdb=" O   ALA D 235 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 114
      removed outlier: 5.940A  pdb=" N   LEU E  40 " --> pdb=" O   GLY E  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR E  81 " --> pdb=" O   LEU E  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY E  42 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE E  83 " --> pdb=" O   GLY E  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG E  44 " --> pdb=" O   ILE E  83 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY E  78 " --> pdb=" O   HIS E  32 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS E  26 " --> pdb=" O   ILE E  84 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS F  26 " --> pdb=" O   ILE F  84 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY F  78 " --> pdb=" O   HIS F  32 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU F  40 " --> pdb=" O   GLY F  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR F  81 " --> pdb=" O   LEU F  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY F  42 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE F  83 " --> pdb=" O   GLY F  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG F  44 " --> pdb=" O   ILE F  83 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL E 175 " --> pdb=" O   ILE E 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA E 235 " --> pdb=" O   VAL E 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA E 177 " --> pdb=" O   ALA E 235 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL F 175 " --> pdb=" O   ILE F 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA F 235 " --> pdb=" O   VAL F 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA F 177 " --> pdb=" O   ALA F 235 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 110 through 114
      removed outlier: 5.940A  pdb=" N   LEU G  40 " --> pdb=" O   GLY G  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR G  81 " --> pdb=" O   LEU G  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY G  42 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE G  83 " --> pdb=" O   GLY G  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG G  44 " --> pdb=" O   ILE G  83 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY G  78 " --> pdb=" O   HIS G  32 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS G  26 " --> pdb=" O   ILE G  84 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LYS H  26 " --> pdb=" O   ILE H  84 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY H  78 " --> pdb=" O   HIS H  32 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU H  40 " --> pdb=" O   GLY H  79 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR H  81 " --> pdb=" O   LEU H  40 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLY H  42 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE H  83 " --> pdb=" O   GLY H  42 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG H  44 " --> pdb=" O   ILE H  83 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL G 175 " --> pdb=" O   ILE G 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA G 235 " --> pdb=" O   VAL G 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA G 177 " --> pdb=" O   ALA G 235 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 198 through 202
      removed outlier: 6.752A  pdb=" N   VAL H 175 " --> pdb=" O   ILE H 233 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA H 235 " --> pdb=" O   VAL H 175 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA H 177 " --> pdb=" O   ALA H 235 " (cutoff:3.500A)

    1128 hydrogen bonds defined for protein.
    3256 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.08

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 4008
        1.31 -     1.43: 6056
        1.43 -     1.56: 13336
        1.56 -     1.69: 48
        1.69 -     1.81: 240
  Bond restraints: 23688
  Sorted by residual:
  bond pdb=" C3B NAD G 400 "
       pdb=" C4B NAD G 400 "
    ideal  model  delta    sigma   weight residual
    1.523  1.293  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C3B NAD C 400 "
       pdb=" C4B NAD C 400 "
    ideal  model  delta    sigma   weight residual
    1.523  1.293  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C3B NAD H 400 "
       pdb=" C4B NAD H 400 "
    ideal  model  delta    sigma   weight residual
    1.523  1.293  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C3B NAD A 400 "
       pdb=" C4B NAD A 400 "
    ideal  model  delta    sigma   weight residual
    1.523  1.293  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C3B NAD F 400 "
       pdb=" C4B NAD F 400 "
    ideal  model  delta    sigma   weight residual
    1.523  1.293  0.230 2.00e-02 2.50e+03 1.32e+02
  ... (remaining 23683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 31193
        3.37 -     6.74: 655
        6.74 -    10.11: 104
       10.11 -    13.48: 48
       13.48 -    16.85: 24
  Bond angle restraints: 32024
  Sorted by residual:
  angle pdb=" N1A NAD C 400 "
        pdb=" C6A NAD C 400 "
        pdb=" N6A NAD C 400 "
      ideal   model   delta    sigma   weight residual
     119.35  102.50   16.85 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" N1A NAD D 400 "
        pdb=" C6A NAD D 400 "
        pdb=" N6A NAD D 400 "
      ideal   model   delta    sigma   weight residual
     119.35  102.52   16.83 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" N1A NAD E 400 "
        pdb=" C6A NAD E 400 "
        pdb=" N6A NAD E 400 "
      ideal   model   delta    sigma   weight residual
     119.35  102.54   16.81 3.00e+00 1.11e-01 3.14e+01
  angle pdb=" N1A NAD H 400 "
        pdb=" C6A NAD H 400 "
        pdb=" N6A NAD H 400 "
      ideal   model   delta    sigma   weight residual
     119.35  102.54   16.81 3.00e+00 1.11e-01 3.14e+01
  angle pdb=" N1A NAD F 400 "
        pdb=" C6A NAD F 400 "
        pdb=" N6A NAD F 400 "
      ideal   model   delta    sigma   weight residual
     119.35  102.54   16.81 3.00e+00 1.11e-01 3.14e+01
  ... (remaining 32019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 13688
       17.20 -    34.39: 624
       34.39 -    51.59: 168
       51.59 -    68.79: 96
       68.79 -    85.98: 48
  Dihedral angle restraints: 14624
    sinusoidal: 6176
      harmonic: 8448
  Sorted by residual:
  dihedral pdb=" CA  ILE E 136 "
           pdb=" C   ILE E 136 "
           pdb=" N   SER E 137 "
           pdb=" CA  SER E 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.06  -27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  ILE H 136 "
           pdb=" C   ILE H 136 "
           pdb=" N   SER H 137 "
           pdb=" CA  SER H 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.06  -27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  ILE B 136 "
           pdb=" C   ILE B 136 "
           pdb=" N   SER B 137 "
           pdb=" CA  SER B 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.06  -27.94     0      5.00e+00 4.00e-02 3.12e+01
  ... (remaining 14621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 2280
       0.064 -    0.128: 964
       0.128 -    0.191: 188
       0.191 -    0.255: 0
       0.255 -    0.319: 16
  Chirality restraints: 3448
  Sorted by residual:
  chirality pdb=" C3B NAD B 400 "
            pdb=" C2B NAD B 400 "
            pdb=" C4B NAD B 400 "
            pdb=" O3B NAD B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.39   -0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" C3B NAD D 400 "
            pdb=" C2B NAD D 400 "
            pdb=" C4B NAD D 400 "
            pdb=" O3B NAD D 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.39   -0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" C3D NAD D 400 "
            pdb=" C2D NAD D 400 "
            pdb=" C4D NAD D 400 "
            pdb=" O3D NAD D 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.41   -0.32 2.00e-01 2.50e+01 2.53e+00
  ... (remaining 3445 not shown)

  Planarity restraints: 4200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY F  37 "   -0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO F  38 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO F  38 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO F  38 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D  37 "   -0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO D  38 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO D  38 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D  38 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  37 "   -0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO B  38 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B  38 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  38 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 4197 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 5725
        2.79 -     3.32: 20148
        3.32 -     3.84: 37426
        3.84 -     4.37: 44949
        4.37 -     4.90: 79882
  Nonbonded interactions: 188130
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  43 "
            pdb=" OG1 THR H 112 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG1 THR A  43 "
            pdb=" OG1 THR A 112 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG1 THR C  43 "
            pdb=" OG1 THR C 112 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG1 THR B  43 "
            pdb=" OG1 THR B 112 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG1 THR F  43 "
            pdb=" OG1 THR F 112 "
     model   vdw
     2.261 3.040
  ... (remaining 188125 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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=0.50 max=1.00 mean=0.99
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:             0.480
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.460
  Find NCS groups from input model:        0.230
  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:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
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      :  0.016   0.230  23688  Z= 0.695
  Angle     :  1.356  16.851  32024  Z= 0.662
  Chirality :  0.071   0.319   3448
  Planarity :  0.007   0.056   4200
  Dihedral  : 13.306  85.981   9280
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  4.11 %
    Favored  : 94.86 %
  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: -3.92 (0.12), residues: 2912
  helix: -2.54 (0.10), residues: 1368
  sheet: -1.72 (0.19), residues: 504
  loop : -2.85 (0.15), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG E 190 
 TYR   0.035   0.005   TYR B 186 
 PHE   0.031   0.006   PHE C 102 
 TRP   0.017   0.004   TRP G  46 
 HIS   0.012   0.003   HIS G 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.01550 (23688)
  covalent geometry    : angle       1.35630 (32024)
  hydrogen bonds       : bond        0.14455 ( 1128)
  hydrogen bonds       : angle       6.29663 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  584 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 584
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A  346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt)
REVERT: B  346 MET cc_start: 0.7944 (mmm) cc_final: 0.7740 (mmt)
REVERT: C  346 MET cc_start: 0.7941 (mmm) cc_final: 0.7737 (mmt)
REVERT: D  346 MET cc_start: 0.7945 (mmm) cc_final: 0.7740 (mmt)
REVERT: E  346 MET cc_start: 0.7943 (mmm) cc_final: 0.7737 (mmt)
REVERT: F  346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt)
REVERT: G  346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt)
REVERT: H  346 MET cc_start: 0.7943 (mmm) cc_final: 0.7736 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 584
  average time/residue: 0.1709
  time to fit residues: 151.9413
Evaluate side-chains
  384 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 384
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 197 optimal weight:    6.9990
   chunk 215 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 132 optimal weight:    0.5980
   chunk 261 optimal weight:    0.9980
   chunk 248 optimal weight:    0.0570
   chunk 207 optimal weight:   10.0000
   chunk 155 optimal weight:    1.9990
   chunk 244 optimal weight:    0.9980
   chunk 183 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 179 GLN
A 193 HIS
A 293 ASN
A 302 ASN
** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 145 ASN
B 179 GLN
B 193 HIS
B 293 ASN
B 302 ASN
** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 ASN
C 179 GLN
C 193 HIS
C 293 ASN
C 302 ASN
** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 145 ASN
D 179 GLN
D 193 HIS
D 293 ASN
D 302 ASN
** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 145 ASN
E 179 GLN
E 193 HIS
E 293 ASN
E 302 ASN
** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 145 ASN
F 179 GLN
F 193 HIS
F 293 ASN
F 302 ASN
** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 145 ASN
G 179 GLN
G 193 HIS
G 293 ASN
G 302 ASN
** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 145 ASN
H 179 GLN
H 193 HIS
H 293 ASN
H 302 ASN
** H 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 40

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.177941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.132415 restraints weight = 108240.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 8.47
r_work: 0.2722 rms_B_bonded: 6.68 restraints_weight: 2.0000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  23688  Z= 0.118
  Angle     :  0.619   6.485  32024  Z= 0.322
  Chirality :  0.044   0.149   3448
  Planarity :  0.004   0.038   4200
  Dihedral  :  9.694  53.804   3752
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.70 %
    Favored  : 86.56 %
  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: -1.92 (0.14), residues: 2912
  helix: -0.68 (0.13), residues: 1416
  sheet: -0.97 (0.21), residues: 512
  loop : -2.12 (0.17), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 347 
 TYR   0.012   0.001   TYR D   6 
 PHE   0.014   0.002   PHE A  99 
 TRP   0.008   0.002   TRP A  46 
 HIS   0.006   0.001   HIS G 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (23688)
  covalent geometry    : angle       0.61887 (32024)
  hydrogen bonds       : bond        0.03935 ( 1128)
  hydrogen bonds       : angle       4.77475 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  448 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 408
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  219 LYS cc_start: 0.7304 (mttt) cc_final: 0.7050 (mttp)
REVERT: A  346 MET cc_start: 0.8893 (mmm) cc_final: 0.8656 (mmm)
REVERT: A  363 ARG cc_start: 0.8052 (tmt170) cc_final: 0.7810 (tmt170)
REVERT: B  219 LYS cc_start: 0.7312 (mttt) cc_final: 0.7060 (mttp)
REVERT: B  346 MET cc_start: 0.8903 (mmm) cc_final: 0.8668 (mmm)
REVERT: B  363 ARG cc_start: 0.8055 (tmt170) cc_final: 0.7816 (tmt170)
REVERT: C  219 LYS cc_start: 0.7325 (mttt) cc_final: 0.7072 (mttp)
REVERT: C  346 MET cc_start: 0.8896 (mmm) cc_final: 0.8660 (mmm)
REVERT: C  363 ARG cc_start: 0.8049 (tmt170) cc_final: 0.7806 (tmt170)
REVERT: D  219 LYS cc_start: 0.7320 (mttt) cc_final: 0.7067 (mttp)
REVERT: D  346 MET cc_start: 0.8903 (mmm) cc_final: 0.8668 (mmm)
REVERT: D  363 ARG cc_start: 0.8033 (tmt170) cc_final: 0.7793 (tmt170)
REVERT: E  219 LYS cc_start: 0.7317 (mttt) cc_final: 0.7061 (mttp)
REVERT: E  346 MET cc_start: 0.8895 (mmm) cc_final: 0.8657 (mmm)
REVERT: E  363 ARG cc_start: 0.8031 (tmt170) cc_final: 0.7790 (tmt170)
REVERT: F  219 LYS cc_start: 0.7322 (mttt) cc_final: 0.7067 (mttp)
REVERT: F  346 MET cc_start: 0.8907 (mmm) cc_final: 0.8669 (mmm)
REVERT: F  363 ARG cc_start: 0.8052 (tmt170) cc_final: 0.7822 (tmt170)
REVERT: G  219 LYS cc_start: 0.7307 (mttt) cc_final: 0.7055 (mttp)
REVERT: G  346 MET cc_start: 0.8890 (mmm) cc_final: 0.8655 (mmm)
REVERT: G  363 ARG cc_start: 0.8043 (tmt170) cc_final: 0.7804 (tmt170)
REVERT: H  219 LYS cc_start: 0.7320 (mttt) cc_final: 0.7068 (mttp)
REVERT: H  346 MET cc_start: 0.8915 (mmm) cc_final: 0.8679 (mmm)
REVERT: H  363 ARG cc_start: 0.8035 (tmt170) cc_final: 0.7795 (tmt170)
  outliers start: 40
  outliers final: 32
  residues processed: 432
  average time/residue: 0.1688
  time to fit residues: 112.3004
Evaluate side-chains
  378 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 346
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain D residue    8 GLU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain E residue    8 GLU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  114 GLU
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain F residue    8 GLU
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue  114 GLU
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue  114 GLU
Chi-restraints excluded: chain G residue  147 SER
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue  114 GLU
Chi-restraints excluded: chain H residue  147 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 174 optimal weight:   10.0000
   chunk 187 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 135 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 139 optimal weight:    0.7980
   chunk 132 optimal weight:    5.9990
   chunk 233 optimal weight:    9.9990
   chunk 169 optimal weight:   20.0000
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
A 107 ASN
A 193 HIS
A 359 HIS
B  32 HIS
B 107 ASN
B 193 HIS
B 359 HIS
C  32 HIS
C 107 ASN
C 193 HIS
C 359 HIS
D  32 HIS
D 107 ASN
D 193 HIS
D 359 HIS
E  32 HIS
E 107 ASN
E 179 GLN
E 193 HIS
E 359 HIS
F  32 HIS
F 107 ASN
F 193 HIS
F 359 HIS
G  32 HIS
G 107 ASN
G 193 HIS
G 359 HIS
H  32 HIS
H 107 ASN
H 193 HIS
H 359 HIS

Total number of N/Q/H flips: 33

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.171397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.101479 restraints weight = 104598.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 4.77
r_work: 0.2744 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044  23688  Z= 0.287
  Angle     :  0.690   6.776  32024  Z= 0.356
  Chirality :  0.048   0.149   3448
  Planarity :  0.005   0.035   4200
  Dihedral  :  8.518  54.549   3752
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 11.39 %
    Favored  : 84.50 %
  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: -1.40 (0.14), residues: 2912
  helix: -0.09 (0.13), residues: 1424
  sheet: -1.18 (0.21), residues: 496
  loop : -1.87 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 190 
 TYR   0.013   0.002   TYR G 284 
 PHE   0.012   0.002   PHE D   4 
 TRP   0.012   0.003   TRP D  46 
 HIS   0.006   0.001   HIS H 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 (23688)
  covalent geometry    : angle       0.69028 (32024)
  hydrogen bonds       : bond        0.05247 ( 1128)
  hydrogen bonds       : angle       4.67654 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  480 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 408
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   46 TRP cc_start: 0.8368 (t-100) cc_final: 0.7772 (t-100)
REVERT: A  219 LYS cc_start: 0.7316 (mttt) cc_final: 0.6944 (mttp)
REVERT: B   46 TRP cc_start: 0.8374 (t-100) cc_final: 0.7779 (t-100)
REVERT: B  219 LYS cc_start: 0.7338 (mttt) cc_final: 0.6966 (mttp)
REVERT: C   46 TRP cc_start: 0.8364 (t-100) cc_final: 0.7771 (t-100)
REVERT: C  219 LYS cc_start: 0.7326 (mttt) cc_final: 0.6953 (mttp)
REVERT: D   46 TRP cc_start: 0.8384 (t-100) cc_final: 0.7791 (t-100)
REVERT: D  219 LYS cc_start: 0.7318 (mttt) cc_final: 0.6946 (mttp)
REVERT: E   46 TRP cc_start: 0.8370 (t-100) cc_final: 0.7775 (t-100)
REVERT: E  219 LYS cc_start: 0.7332 (mttt) cc_final: 0.6962 (mttp)
REVERT: F   46 TRP cc_start: 0.8381 (t-100) cc_final: 0.7788 (t-100)
REVERT: F  219 LYS cc_start: 0.7337 (mttt) cc_final: 0.6968 (mttp)
REVERT: G   46 TRP cc_start: 0.8370 (t-100) cc_final: 0.7776 (t-100)
REVERT: G  219 LYS cc_start: 0.7317 (mttt) cc_final: 0.6947 (mttp)
REVERT: H   46 TRP cc_start: 0.8374 (t-100) cc_final: 0.7778 (t-100)
REVERT: H  219 LYS cc_start: 0.7340 (mttt) cc_final: 0.6968 (mttp)
  outliers start: 72
  outliers final: 64
  residues processed: 456
  average time/residue: 0.1574
  time to fit residues: 112.9819
Evaluate side-chains
  448 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 384
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   89 LYS
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  286 ILE
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   89 LYS
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  125 ILE
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  286 ILE
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   89 LYS
Chi-restraints excluded: chain E residue  114 GLU
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  242 ILE
Chi-restraints excluded: chain E residue  286 ILE
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue   89 LYS
Chi-restraints excluded: chain F residue  114 GLU
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain F residue  242 ILE
Chi-restraints excluded: chain F residue  286 ILE
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue   61 LEU
Chi-restraints excluded: chain G residue   89 LYS
Chi-restraints excluded: chain G residue  114 GLU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain G residue  242 ILE
Chi-restraints excluded: chain G residue  286 ILE
Chi-restraints excluded: chain G residue  329 ILE
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue   89 LYS
Chi-restraints excluded: chain H residue  114 GLU
Chi-restraints excluded: chain H residue  125 ILE
Chi-restraints excluded: chain H residue  242 ILE
Chi-restraints excluded: chain H residue  286 ILE
Chi-restraints excluded: chain H residue  329 ILE
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 225 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 217 optimal weight:    0.9990
   chunk 216 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   chunk 285 optimal weight:    4.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
B 179 GLN
C 179 GLN
D 179 GLN
F 179 GLN
G 179 GLN
H 179 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.175000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.102976 restraints weight = 109997.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 5.01
r_work: 0.2788 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  23688  Z= 0.133
  Angle     :  0.566   6.005  32024  Z= 0.295
  Chirality :  0.044   0.146   3448
  Planarity :  0.003   0.031   4200
  Dihedral  :  7.993  52.350   3752
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.21 %
    Favored  : 83.13 %
  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: -0.71 (0.15), residues: 2912
  helix:  0.52 (0.13), residues: 1424
  sheet: -0.88 (0.21), residues: 496
  loop : -1.61 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 347 
 TYR   0.007   0.001   TYR D 132 
 PHE   0.010   0.001   PHE A  99 
 TRP   0.007   0.001   TRP A  46 
 HIS   0.002   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (23688)
  covalent geometry    : angle       0.56636 (32024)
  hydrogen bonds       : bond        0.03695 ( 1128)
  hydrogen bonds       : angle       4.35159 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  412 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 374
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8784 (tp)
REVERT: A   46 TRP cc_start: 0.8313 (t-100) cc_final: 0.7756 (t-100)
REVERT: A  219 LYS cc_start: 0.7285 (mttt) cc_final: 0.6907 (mttp)
REVERT: A  227 TYR cc_start: 0.8333 (m-80) cc_final: 0.8119 (m-80)
REVERT: B   16 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8788 (tp)
REVERT: B   46 TRP cc_start: 0.8318 (t-100) cc_final: 0.7757 (t-100)
REVERT: B  219 LYS cc_start: 0.7288 (mttt) cc_final: 0.6909 (mttp)
REVERT: B  227 TYR cc_start: 0.8335 (m-80) cc_final: 0.8120 (m-80)
REVERT: C   16 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8782 (tp)
REVERT: C   46 TRP cc_start: 0.8305 (t-100) cc_final: 0.7745 (t-100)
REVERT: C  219 LYS cc_start: 0.7294 (mttt) cc_final: 0.6918 (mttp)
REVERT: C  227 TYR cc_start: 0.8338 (m-80) cc_final: 0.8120 (m-80)
REVERT: D   16 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8787 (tp)
REVERT: D   46 TRP cc_start: 0.8318 (t-100) cc_final: 0.7760 (t-100)
REVERT: D  219 LYS cc_start: 0.7283 (mttt) cc_final: 0.6904 (mttp)
REVERT: D  227 TYR cc_start: 0.8340 (m-80) cc_final: 0.8127 (m-80)
REVERT: E   16 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8782 (tp)
REVERT: E   46 TRP cc_start: 0.8300 (t-100) cc_final: 0.7743 (t-100)
REVERT: E  219 LYS cc_start: 0.7285 (mttt) cc_final: 0.6907 (mttp)
REVERT: E  227 TYR cc_start: 0.8333 (m-80) cc_final: 0.8123 (m-80)
REVERT: F   16 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (tp)
REVERT: F   46 TRP cc_start: 0.8304 (t-100) cc_final: 0.7746 (t-100)
REVERT: F  219 LYS cc_start: 0.7287 (mttt) cc_final: 0.6910 (mttp)
REVERT: F  227 TYR cc_start: 0.8340 (m-80) cc_final: 0.8130 (m-80)
REVERT: G   16 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8789 (tp)
REVERT: G   46 TRP cc_start: 0.8303 (t-100) cc_final: 0.7745 (t-100)
REVERT: G  219 LYS cc_start: 0.7289 (mttt) cc_final: 0.6912 (mttp)
REVERT: G  227 TYR cc_start: 0.8338 (m-80) cc_final: 0.8124 (m-80)
REVERT: H   16 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8782 (tp)
REVERT: H   46 TRP cc_start: 0.8315 (t-100) cc_final: 0.7752 (t-100)
REVERT: H  219 LYS cc_start: 0.7293 (mttt) cc_final: 0.6913 (mttp)
REVERT: H  227 TYR cc_start: 0.8338 (m-80) cc_final: 0.8126 (m-80)
  outliers start: 38
  outliers final: 18
  residues processed: 406
  average time/residue: 0.1611
  time to fit residues: 103.6041
Evaluate side-chains
  381 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 355
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue    8 GLU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue  114 GLU
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue    8 GLU
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue  114 GLU
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue  114 GLU
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue   16 LEU
Chi-restraints excluded: chain H residue  114 GLU
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 240 optimal weight:    0.0270
   chunk 84 optimal weight:    4.9990
   chunk 215 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   chunk 165 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 271 optimal weight:   20.0000
   chunk 132 optimal weight:    0.0770
   chunk 189 optimal weight:    1.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
H 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.176409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.130937 restraints weight = 121620.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 9.01
r_work: 0.2681 rms_B_bonded: 6.64 restraints_weight: 2.0000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  23688  Z= 0.107
  Angle     :  0.531   5.760  32024  Z= 0.276
  Chirality :  0.042   0.142   3448
  Planarity :  0.003   0.029   4200
  Dihedral  :  7.622  51.621   3752
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.11 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.27 (0.15), residues: 2912
  helix:  0.87 (0.14), residues: 1424
  sheet: -0.53 (0.22), residues: 496
  loop : -1.46 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 347 
 TYR   0.007   0.001   TYR G 132 
 PHE   0.010   0.001   PHE A  99 
 TRP   0.004   0.001   TRP H  46 
 HIS   0.002   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (23688)
  covalent geometry    : angle       0.53112 (32024)
  hydrogen bonds       : bond        0.03200 ( 1128)
  hydrogen bonds       : angle       4.15257 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 360
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A   46 TRP cc_start: 0.8351 (t-100) cc_final: 0.7792 (t-100)
REVERT: A   65 MET cc_start: 0.9319 (mmm) cc_final: 0.9022 (tpt)
REVERT: A  219 LYS cc_start: 0.7541 (mttt) cc_final: 0.7313 (mttp)
REVERT: A  227 TYR cc_start: 0.8232 (m-80) cc_final: 0.8024 (m-80)
REVERT: B   46 TRP cc_start: 0.8383 (t-100) cc_final: 0.7800 (t-100)
REVERT: B   65 MET cc_start: 0.9327 (mmm) cc_final: 0.9031 (tpt)
REVERT: B  219 LYS cc_start: 0.7530 (mttt) cc_final: 0.7300 (mttp)
REVERT: B  227 TYR cc_start: 0.8240 (m-80) cc_final: 0.8022 (m-80)
REVERT: C   46 TRP cc_start: 0.8348 (t-100) cc_final: 0.7795 (t-100)
REVERT: C   65 MET cc_start: 0.9319 (mmm) cc_final: 0.9027 (tpt)
REVERT: C  219 LYS cc_start: 0.7525 (mttt) cc_final: 0.7291 (mttp)
REVERT: C  227 TYR cc_start: 0.8248 (m-80) cc_final: 0.8034 (m-80)
REVERT: D   46 TRP cc_start: 0.8374 (t-100) cc_final: 0.7792 (t-100)
REVERT: D   65 MET cc_start: 0.9322 (mmm) cc_final: 0.9034 (tpt)
REVERT: D  219 LYS cc_start: 0.7524 (mttt) cc_final: 0.7289 (mttp)
REVERT: D  227 TYR cc_start: 0.8245 (m-80) cc_final: 0.8033 (m-80)
REVERT: E   46 TRP cc_start: 0.8349 (t-100) cc_final: 0.7794 (t-100)
REVERT: E   65 MET cc_start: 0.9311 (mmm) cc_final: 0.9023 (tpt)
REVERT: E  219 LYS cc_start: 0.7535 (mttt) cc_final: 0.7301 (mttp)
REVERT: E  227 TYR cc_start: 0.8241 (m-80) cc_final: 0.8035 (m-80)
REVERT: F   46 TRP cc_start: 0.8365 (t-100) cc_final: 0.7786 (t-100)
REVERT: F   65 MET cc_start: 0.9313 (mmm) cc_final: 0.9024 (tpt)
REVERT: F  219 LYS cc_start: 0.7526 (mttt) cc_final: 0.7294 (mttp)
REVERT: F  227 TYR cc_start: 0.8250 (m-80) cc_final: 0.8039 (m-80)
REVERT: G   46 TRP cc_start: 0.8348 (t-100) cc_final: 0.7787 (t-100)
REVERT: G   65 MET cc_start: 0.9314 (mmm) cc_final: 0.9027 (tpt)
REVERT: G  219 LYS cc_start: 0.7533 (mttt) cc_final: 0.7300 (mttp)
REVERT: G  227 TYR cc_start: 0.8251 (m-80) cc_final: 0.8037 (m-80)
REVERT: H   46 TRP cc_start: 0.8383 (t-100) cc_final: 0.7801 (t-100)
REVERT: H   65 MET cc_start: 0.9316 (mmm) cc_final: 0.9025 (tpt)
REVERT: H  219 LYS cc_start: 0.7528 (mttt) cc_final: 0.7297 (mttp)
REVERT: H  227 TYR cc_start: 0.8241 (m-80) cc_final: 0.8032 (m-80)
  outliers start: 61
  outliers final: 14
  residues processed: 398
  average time/residue: 0.1657
  time to fit residues: 103.0378
Evaluate side-chains
  366 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 352
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue    8 GLU
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 206 optimal weight:    2.9990
   chunk 176 optimal weight:    0.9990
   chunk 231 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 236 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 223 optimal weight:   10.0000
   chunk 49 optimal weight:    0.4980
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
B 183 ASN
H 183 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.175377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.109126 restraints weight = 111052.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 5.48
r_work: 0.2794 rms_B_bonded: 5.06 restraints_weight: 2.0000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  23688  Z= 0.117
  Angle     :  0.541   5.480  32024  Z= 0.281
  Chirality :  0.043   0.144   3448
  Planarity :  0.003   0.026   4200
  Dihedral  :  7.506  51.507   3752
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.62 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.06 (0.15), residues: 2912
  helix:  1.12 (0.14), residues: 1424
  sheet: -0.29 (0.23), residues: 496
  loop : -1.33 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 347 
 TYR   0.007   0.001   TYR D 132 
 PHE   0.009   0.001   PHE B  99 
 TRP   0.004   0.001   TRP B  46 
 HIS   0.005   0.001   HIS F 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (23688)
  covalent geometry    : angle       0.54080 (32024)
  hydrogen bonds       : bond        0.03372 ( 1128)
  hydrogen bonds       : angle       4.06756 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 352
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A   46 TRP cc_start: 0.8287 (t-100) cc_final: 0.7795 (t-100)
REVERT: A  219 LYS cc_start: 0.7556 (mttt) cc_final: 0.7342 (mttp)
REVERT: A  272 MET cc_start: 0.6549 (mmm) cc_final: 0.6345 (mmm)
REVERT: B   46 TRP cc_start: 0.8313 (t-100) cc_final: 0.7819 (t-100)
REVERT: B  219 LYS cc_start: 0.7556 (mttt) cc_final: 0.7343 (mttp)
REVERT: B  227 TYR cc_start: 0.8270 (m-80) cc_final: 0.8049 (m-80)
REVERT: C   46 TRP cc_start: 0.8289 (t-100) cc_final: 0.7795 (t-100)
REVERT: C  219 LYS cc_start: 0.7558 (mttt) cc_final: 0.7347 (mttp)
REVERT: D   46 TRP cc_start: 0.8290 (t-100) cc_final: 0.7796 (t-100)
REVERT: D  219 LYS cc_start: 0.7569 (mttt) cc_final: 0.7354 (mttp)
REVERT: D  227 TYR cc_start: 0.8279 (m-80) cc_final: 0.8058 (m-80)
REVERT: D  272 MET cc_start: 0.6542 (mmm) cc_final: 0.6338 (mmm)
REVERT: E   46 TRP cc_start: 0.8297 (t-100) cc_final: 0.7804 (t-100)
REVERT: E  219 LYS cc_start: 0.7568 (mttt) cc_final: 0.7355 (mttp)
REVERT: E  272 MET cc_start: 0.6530 (mmm) cc_final: 0.6326 (mmm)
REVERT: F   46 TRP cc_start: 0.8278 (t-100) cc_final: 0.7786 (t-100)
REVERT: F  219 LYS cc_start: 0.7565 (mttt) cc_final: 0.7352 (mttp)
REVERT: F  227 TYR cc_start: 0.8263 (m-80) cc_final: 0.8041 (m-80)
REVERT: G   46 TRP cc_start: 0.8288 (t-100) cc_final: 0.7794 (t-100)
REVERT: G  219 LYS cc_start: 0.7565 (mttt) cc_final: 0.7351 (mttp)
REVERT: G  227 TYR cc_start: 0.8279 (m-80) cc_final: 0.8058 (m-80)
REVERT: H   46 TRP cc_start: 0.8284 (t-100) cc_final: 0.7792 (t-100)
REVERT: H  219 LYS cc_start: 0.7561 (mttt) cc_final: 0.7350 (mttp)
REVERT: H  227 TYR cc_start: 0.8254 (m-80) cc_final: 0.8035 (m-80)
  outliers start: 32
  outliers final: 19
  residues processed: 362
  average time/residue: 0.1692
  time to fit residues: 95.4852
Evaluate side-chains
  371 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 352
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue    8 GLU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue    8 GLU
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue  329 ILE
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue  329 ILE
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 21 optimal weight:   30.0000
   chunk 268 optimal weight:    5.9990
   chunk 272 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 136 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0670
   chunk 57 optimal weight:   30.0000
   chunk 168 optimal weight:    4.9990
   chunk 134 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 249 optimal weight:    1.9990
   overall best weight:    2.4126

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
B 183 ASN
C 183 ASN
D 183 ASN
E 183 ASN
F 183 ASN
G 183 ASN
H 183 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.173302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.106510 restraints weight = 108889.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 5.43
r_work: 0.2757 rms_B_bonded: 5.04 restraints_weight: 2.0000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  23688  Z= 0.173
  Angle     :  0.576   5.443  32024  Z= 0.298
  Chirality :  0.044   0.147   3448
  Planarity :  0.003   0.025   4200
  Dihedral  :  7.574  52.611   3752
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.62 %
    Favored  : 80.95 %
  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:  0.11 (0.15), residues: 2912
  helix:  1.15 (0.13), residues: 1424
  sheet: -0.23 (0.23), residues: 496
  loop : -1.30 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 347 
 TYR   0.010   0.001   TYR E 284 
 PHE   0.008   0.001   PHE B  99 
 TRP   0.006   0.001   TRP F  46 
 HIS   0.003   0.001   HIS B 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (23688)
  covalent geometry    : angle       0.57649 (32024)
  hydrogen bonds       : bond        0.04019 ( 1128)
  hydrogen bonds       : angle       4.11293 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  400 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 344
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   46 TRP cc_start: 0.8239 (t-100) cc_final: 0.7692 (t-100)
REVERT: B   46 TRP cc_start: 0.8234 (t-100) cc_final: 0.7693 (t-100)
REVERT: C   46 TRP cc_start: 0.8225 (t-100) cc_final: 0.7679 (t-100)
REVERT: D   46 TRP cc_start: 0.8241 (t-100) cc_final: 0.7694 (t-100)
REVERT: D  219 LYS cc_start: 0.7536 (mttt) cc_final: 0.7335 (mttp)
REVERT: E   46 TRP cc_start: 0.8235 (t-100) cc_final: 0.7686 (t-100)
REVERT: F   46 TRP cc_start: 0.8235 (t-100) cc_final: 0.7688 (t-100)
REVERT: G   46 TRP cc_start: 0.8229 (t-100) cc_final: 0.7681 (t-100)
REVERT: H   46 TRP cc_start: 0.8240 (t-100) cc_final: 0.7696 (t-100)
  outliers start: 56
  outliers final: 34
  residues processed: 374
  average time/residue: 0.1688
  time to fit residues: 98.1654
Evaluate side-chains
  371 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 337
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  183 ASN
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue  125 ILE
Chi-restraints excluded: chain D residue  183 ASN
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  183 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain F residue  183 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain G residue  183 ASN
Chi-restraints excluded: chain G residue  329 ILE
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue  125 ILE
Chi-restraints excluded: chain H residue  183 ASN
Chi-restraints excluded: chain H residue  329 ILE
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 142 optimal weight:    7.9990
   chunk 261 optimal weight:    2.9990
   chunk 183 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 281 optimal weight:    2.9990
   chunk 278 optimal weight:    8.9990
   chunk 168 optimal weight:    4.9990
   chunk 25 optimal weight:   20.0000
   chunk 205 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
B 183 ASN
C 183 ASN
D 183 ASN
E 183 ASN
F 183 ASN
G 183 ASN
H 183 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.171437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.102653 restraints weight = 118748.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 5.49
r_work: 0.2714 rms_B_bonded: 5.07 restraints_weight: 2.0000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  23688  Z= 0.268
  Angle     :  0.657   6.725  32024  Z= 0.336
  Chirality :  0.047   0.166   3448
  Planarity :  0.004   0.032   4200
  Dihedral  :  7.745  53.426   3752
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.24 %
    Favored  : 80.86 %
  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: -0.03 (0.15), residues: 2912
  helix:  0.97 (0.13), residues: 1424
  sheet: -0.23 (0.23), residues: 496
  loop : -1.29 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 109 
 TYR   0.013   0.002   TYR G 284 
 PHE   0.010   0.002   PHE D  99 
 TRP   0.008   0.002   TRP D  46 
 HIS   0.006   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 (23688)
  covalent geometry    : angle       0.65652 (32024)
  hydrogen bonds       : bond        0.04669 ( 1128)
  hydrogen bonds       : angle       4.27006 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 354
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   46 TRP cc_start: 0.8389 (t-100) cc_final: 0.7799 (t-100)
REVERT: A  308 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7173 (tptm)
REVERT: B   46 TRP cc_start: 0.8393 (t-100) cc_final: 0.7800 (t-100)
REVERT: B  308 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7178 (tptm)
REVERT: C   46 TRP cc_start: 0.8371 (t-100) cc_final: 0.7776 (t-100)
REVERT: C  308 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7173 (tptm)
REVERT: D   46 TRP cc_start: 0.8391 (t-100) cc_final: 0.7794 (t-100)
REVERT: D  219 LYS cc_start: 0.7419 (mttt) cc_final: 0.7140 (mttp)
REVERT: D  308 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7165 (tptm)
REVERT: E   46 TRP cc_start: 0.8365 (t-100) cc_final: 0.7771 (t-100)
REVERT: E  308 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7168 (tptm)
REVERT: F   46 TRP cc_start: 0.8375 (t-100) cc_final: 0.7777 (t-100)
REVERT: F  308 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7171 (tptm)
REVERT: G   46 TRP cc_start: 0.8378 (t-100) cc_final: 0.7780 (t-100)
REVERT: G  308 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7171 (tptm)
REVERT: H   46 TRP cc_start: 0.8373 (t-100) cc_final: 0.7778 (t-100)
REVERT: H  308 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7178 (tptm)
  outliers start: 67
  outliers final: 47
  residues processed: 391
  average time/residue: 0.1795
  time to fit residues: 107.6090
Evaluate side-chains
  401 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 354
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  219 LYS
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  219 LYS
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  125 ILE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue  114 GLU
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue  114 GLU
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue  114 GLU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain G residue  202 THR
Chi-restraints excluded: chain G residue  219 LYS
Chi-restraints excluded: chain G residue  329 ILE
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue  114 GLU
Chi-restraints excluded: chain H residue  125 ILE
Chi-restraints excluded: chain H residue  202 THR
Chi-restraints excluded: chain H residue  219 LYS
Chi-restraints excluded: chain H residue  329 ILE
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 183 optimal weight:    1.9990
   chunk 123 optimal weight:    5.9990
   chunk 194 optimal weight:    0.9990
   chunk 153 optimal weight:    5.9990
   chunk 260 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
B 183 ASN
C 183 ASN
D 183 ASN
E 183 ASN
F 183 ASN
G 183 ASN
H 183 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.173568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.104626 restraints weight = 97810.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 4.53
r_work: 0.2800 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  23688  Z= 0.146
  Angle     :  0.572   6.741  32024  Z= 0.295
  Chirality :  0.044   0.154   3448
  Planarity :  0.003   0.026   4200
  Dihedral  :  7.535  51.472   3752
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.10 %
    Favored  : 81.21 %
  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:  0.16 (0.15), residues: 2912
  helix:  1.16 (0.13), residues: 1424
  sheet: -0.20 (0.23), residues: 496
  loop : -1.22 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 347 
 TYR   0.007   0.001   TYR A 132 
 PHE   0.010   0.001   PHE H  99 
 TRP   0.005   0.001   TRP A  46 
 HIS   0.004   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (23688)
  covalent geometry    : angle       0.57154 (32024)
  hydrogen bonds       : bond        0.03749 ( 1128)
  hydrogen bonds       : angle       4.09840 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 347
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   46 TRP cc_start: 0.8219 (t-100) cc_final: 0.7643 (t-100)
REVERT: A   65 MET cc_start: 0.9361 (mmm) cc_final: 0.9027 (tpt)
REVERT: B   46 TRP cc_start: 0.8232 (t-100) cc_final: 0.7655 (t-100)
REVERT: B   65 MET cc_start: 0.9362 (mmm) cc_final: 0.9029 (tpt)
REVERT: C   46 TRP cc_start: 0.8225 (t-100) cc_final: 0.7646 (t-100)
REVERT: C   65 MET cc_start: 0.9363 (mmm) cc_final: 0.9032 (tpt)
REVERT: D   46 TRP cc_start: 0.8230 (t-100) cc_final: 0.7648 (t-100)
REVERT: D   65 MET cc_start: 0.9361 (mmm) cc_final: 0.9029 (tpt)
REVERT: D  219 LYS cc_start: 0.7431 (mttt) cc_final: 0.7177 (mttp)
REVERT: E   46 TRP cc_start: 0.8227 (t-100) cc_final: 0.7644 (t-100)
REVERT: E   65 MET cc_start: 0.9356 (mmm) cc_final: 0.9023 (tpt)
REVERT: F   46 TRP cc_start: 0.8228 (t-100) cc_final: 0.7644 (t-100)
REVERT: F   65 MET cc_start: 0.9365 (mmm) cc_final: 0.9034 (tpt)
REVERT: G   46 TRP cc_start: 0.8215 (t-100) cc_final: 0.7636 (t-100)
REVERT: G   65 MET cc_start: 0.9357 (mmm) cc_final: 0.9023 (tpt)
REVERT: H   46 TRP cc_start: 0.8230 (t-100) cc_final: 0.7651 (t-100)
REVERT: H   65 MET cc_start: 0.9358 (mmm) cc_final: 0.9027 (tpt)
  outliers start: 39
  outliers final: 39
  residues processed: 376
  average time/residue: 0.1631
  time to fit residues: 96.0279
Evaluate side-chains
  386 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 347
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  219 LYS
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  219 LYS
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  125 ILE
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue  114 GLU
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue  114 GLU
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue  114 GLU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain G residue  219 LYS
Chi-restraints excluded: chain G residue  329 ILE
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue  114 GLU
Chi-restraints excluded: chain H residue  125 ILE
Chi-restraints excluded: chain H residue  219 LYS
Chi-restraints excluded: chain H residue  329 ILE
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 268 optimal weight:    3.9990
   chunk 150 optimal weight:    3.9990
   chunk 224 optimal weight:    4.9990
   chunk 153 optimal weight:    0.6980
   chunk 118 optimal weight:    0.7980
   chunk 131 optimal weight:   20.0000
   chunk 171 optimal weight:    0.5980
   chunk 179 optimal weight:    0.0370
   chunk 67 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 226 optimal weight:    0.8980
   overall best weight:    0.6058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.177296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.104251 restraints weight = 99558.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 4.78
r_work: 0.2836 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  23688  Z= 0.105
  Angle     :  0.536   7.011  32024  Z= 0.278
  Chirality :  0.043   0.147   3448
  Planarity :  0.003   0.028   4200
  Dihedral  :  7.235  50.392   3752
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.44 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.15), residues: 2912
  helix:  1.35 (0.14), residues: 1424
  sheet: -0.03 (0.24), residues: 496
  loop : -1.16 (0.18), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 347 
 TYR   0.008   0.001   TYR H 132 
 PHE   0.009   0.001   PHE A  99 
 TRP   0.002   0.000   TRP D  46 
 HIS   0.005   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (23688)
  covalent geometry    : angle       0.53605 (32024)
  hydrogen bonds       : bond        0.03026 ( 1128)
  hydrogen bonds       : angle       3.89416 ( 3256)

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

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

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5824 Ramachandran restraints generated.
    2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 362
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.9100 (tt) cc_final: 0.8872 (tp)
REVERT: A   46 TRP cc_start: 0.8153 (t-100) cc_final: 0.7619 (t-100)
REVERT: A   65 MET cc_start: 0.9299 (mmm) cc_final: 0.8965 (tpt)
REVERT: A  194 GLU cc_start: 0.7685 (tp30) cc_final: 0.7239 (mt-10)
REVERT: B   16 LEU cc_start: 0.9098 (tt) cc_final: 0.8870 (tp)
REVERT: B   46 TRP cc_start: 0.8179 (t-100) cc_final: 0.7641 (t-100)
REVERT: B   65 MET cc_start: 0.9311 (mmm) cc_final: 0.8959 (tpt)
REVERT: B  194 GLU cc_start: 0.7697 (tp30) cc_final: 0.7242 (mt-10)
REVERT: C   16 LEU cc_start: 0.9096 (tt) cc_final: 0.8871 (tp)
REVERT: C   46 TRP cc_start: 0.8170 (t-100) cc_final: 0.7630 (t-100)
REVERT: C   65 MET cc_start: 0.9299 (mmm) cc_final: 0.8973 (tpt)
REVERT: C  194 GLU cc_start: 0.7683 (tp30) cc_final: 0.7236 (mt-10)
REVERT: D   16 LEU cc_start: 0.9100 (tt) cc_final: 0.8873 (tp)
REVERT: D   46 TRP cc_start: 0.8152 (t-100) cc_final: 0.7617 (t-100)
REVERT: D   65 MET cc_start: 0.9298 (mmm) cc_final: 0.8969 (tpt)
REVERT: D  194 GLU cc_start: 0.7692 (tp30) cc_final: 0.7234 (mt-10)
REVERT: E   16 LEU cc_start: 0.9102 (tt) cc_final: 0.8876 (tp)
REVERT: E   46 TRP cc_start: 0.8170 (t-100) cc_final: 0.7627 (t-100)
REVERT: E   65 MET cc_start: 0.9313 (mmm) cc_final: 0.8969 (tpt)
REVERT: E  194 GLU cc_start: 0.7677 (tp30) cc_final: 0.7229 (mt-10)
REVERT: F   16 LEU cc_start: 0.9096 (tt) cc_final: 0.8871 (tp)
REVERT: F   46 TRP cc_start: 0.8164 (t-100) cc_final: 0.7630 (t-100)
REVERT: F   65 MET cc_start: 0.9313 (mmm) cc_final: 0.8967 (tpt)
REVERT: F  194 GLU cc_start: 0.7685 (tp30) cc_final: 0.7234 (mt-10)
REVERT: G   46 TRP cc_start: 0.8160 (t-100) cc_final: 0.7623 (t-100)
REVERT: G   65 MET cc_start: 0.9311 (mmm) cc_final: 0.8960 (tpt)
REVERT: G  194 GLU cc_start: 0.7684 (tp30) cc_final: 0.7238 (mt-10)
REVERT: H   46 TRP cc_start: 0.8165 (t-100) cc_final: 0.7630 (t-100)
REVERT: H   65 MET cc_start: 0.9315 (mmm) cc_final: 0.8966 (tpt)
REVERT: H  194 GLU cc_start: 0.7695 (tp30) cc_final: 0.7241 (mt-10)
  outliers start: 29
  outliers final: 21
  residues processed: 383
  average time/residue: 0.1724
  time to fit residues: 103.6521
Evaluate side-chains
  375 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 354
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  219 LYS
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  219 LYS
Chi-restraints excluded: chain C residue  362 SER
Chi-restraints excluded: chain D residue  125 ILE
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  362 SER
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain G residue  219 LYS
Chi-restraints excluded: chain G residue  362 SER
Chi-restraints excluded: chain H residue  125 ILE
Chi-restraints excluded: chain H residue  219 LYS
Chi-restraints excluded: chain H residue  362 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 117 optimal weight:    4.9990
   chunk 215 optimal weight:    0.0050
   chunk 30 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 97 optimal weight:   10.0000
   chunk 173 optimal weight:    8.9990
   chunk 240 optimal weight:    2.9990
   chunk 219 optimal weight:    6.9990
   chunk 213 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 183 optimal weight:    0.7980
   overall best weight:    2.1600

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
D 183 ASN
E 183 ASN
G 183 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.174414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.101906 restraints weight = 107486.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 4.73
r_work: 0.2786 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  23688  Z= 0.161
  Angle     :  0.587   7.839  32024  Z= 0.296
  Chirality :  0.044   0.151   3448
  Planarity :  0.003   0.026   4200
  Dihedral  :  7.363  51.992   3752
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.74 %
    Favored  : 80.95 %
  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:  0.37 (0.15), residues: 2912
  helix:  1.31 (0.13), residues: 1424
  sheet:  0.01 (0.23), residues: 496
  loop : -1.15 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 347 
 TYR   0.012   0.001   TYR C 227 
 PHE   0.008   0.001   PHE A  99 
 TRP   0.002   0.001   TRP B  46 
 HIS   0.004   0.001   HIS E 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (23688)
  covalent geometry    : angle       0.58676 (32024)
  hydrogen bonds       : bond        0.03729 ( 1128)
  hydrogen bonds       : angle       4.01073 ( 3256)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6562.07 seconds
wall clock time: 112 minutes 46.42 seconds (6766.42 seconds total)