Starting phenix.real_space_refine
on Tue Mar  3 23:34:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4k_31714/03_2026/7v4k_31714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4k_31714/03_2026/7v4k_31714.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4k_31714/03_2026/7v4k_31714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4k_31714/03_2026/7v4k_31714.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v4k_31714/03_2026/7v4k_31714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4k_31714/03_2026/7v4k_31714.map"
  }
  resolution = 3.6
  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: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5865      2.51       5
     N    1530      2.21       5
     O    1810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9260
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1852
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1852
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1852
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1852
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 4
    Chain: "E"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1852
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 4
  Time building chain proxies: 2.35, per 1000 atoms: 0.25
  Number of scatterers: 9260
  At special positions: 0
  Unit cell: (120.19, 119.685, 56.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1810      8.00
     N    1530      7.00
     C    5865      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: 0.84
  Conformation dependent library (CDL) restraints added in 352.1 milliseconds
  

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2190

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 16 sheets defined
      35.1% alpha, 34.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 16
      removed outlier: 4.178A  pdb=" N   SER A  15 " --> pdb=" O   ASN A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 61
    Processing helix  chain 'A' and resid 107 through 115
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 168 through 183
      removed outlier: 3.502A  pdb=" N   VAL A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 229
      removed outlier: 3.686A  pdb=" N   GLU A 222 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 3.519A  pdb=" N   ARG A 258 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 254 through 259'
    Processing helix  chain 'A' and resid 339 through 347
      removed outlier: 3.504A  pdb=" N   VAL A 343 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 16
      removed outlier: 4.130A  pdb=" N   SER B  15 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 61
    Processing helix  chain 'B' and resid 107 through 115
    Processing helix  chain 'B' and resid 116 through 123
    Processing helix  chain 'B' and resid 168 through 183
      removed outlier: 3.687A  pdb=" N   VAL B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 229
      removed outlier: 3.561A  pdb=" N   GLU B 222 " --> pdb=" O   ARG B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 259
      removed outlier: 3.667A  pdb=" N   SER B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 351
      removed outlier: 3.575A  pdb=" N   VAL B 343 " --> pdb=" O   ASP B 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 16
      removed outlier: 4.229A  pdb=" N   SER C  15 " --> pdb=" O   ASN C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 61
    Processing helix  chain 'C' and resid 107 through 115
    Processing helix  chain 'C' and resid 116 through 123
    Processing helix  chain 'C' and resid 168 through 183
      removed outlier: 3.713A  pdb=" N   VAL C 172 " --> pdb=" O   GLY C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 229
      removed outlier: 3.525A  pdb=" N   GLU C 222 " --> pdb=" O   ARG C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 259
      removed outlier: 3.557A  pdb=" N   SER C 259 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 351
      removed outlier: 3.552A  pdb=" N   VAL C 343 " --> pdb=" O   ASP C 339 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA C 348 " --> pdb=" O   THR C 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 16
      removed outlier: 4.188A  pdb=" N   SER D  15 " --> pdb=" O   ASN D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 61
    Processing helix  chain 'D' and resid 64 through 67
    Processing helix  chain 'D' and resid 107 through 115
    Processing helix  chain 'D' and resid 116 through 123
    Processing helix  chain 'D' and resid 168 through 183
      removed outlier: 3.724A  pdb=" N   VAL D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 229
      removed outlier: 3.597A  pdb=" N   GLU D 222 " --> pdb=" O   ARG D 218 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 259
      removed outlier: 3.548A  pdb=" N   SER D 259 " --> pdb=" O   LYS D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 339 through 351
      removed outlier: 3.606A  pdb=" N   VAL D 343 " --> pdb=" O   ASP D 339 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 11 through 16
      removed outlier: 4.135A  pdb=" N   SER E  15 " --> pdb=" O   ASN E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 58 through 61
    Processing helix  chain 'E' and resid 107 through 115
    Processing helix  chain 'E' and resid 116 through 123
    Processing helix  chain 'E' and resid 168 through 183
      removed outlier: 3.819A  pdb=" N   VAL E 172 " --> pdb=" O   GLY E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 229
      removed outlier: 3.513A  pdb=" N   GLU E 222 " --> pdb=" O   ARG E 218 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 254 through 259
      removed outlier: 3.608A  pdb=" N   SER E 259 " --> pdb=" O   LYS E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 339 through 351
      removed outlier: 3.503A  pdb=" N   VAL E 343 " --> pdb=" O   ASP E 339 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA E 348 " --> pdb=" O   THR E 344 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40
      removed outlier: 6.356A  pdb=" N   ILE A  20 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   VAL A  90 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   GLU A  22 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   CYS A  92 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   ILE A  24 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ALA A  94 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   ILE A  26 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU A  89 " --> pdb=" O   ILE A  77 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ILE A  77 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   MET A  91 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP A  93 " --> pdb=" O   TYR A  73 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TYR A  73 " --> pdb=" O   ASP A  93 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.985A  pdb=" N   GLN A 201 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE A 189 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU A 199 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN A 130 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 202 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ILE A 128 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206
      removed outlier: 3.924A  pdb=" N   SER A 205 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   TYR A 126 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 33 through 40
      removed outlier: 6.594A  pdb=" N   ILE B  20 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   VAL B  90 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   GLU B  22 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   CYS B  92 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   ILE B  24 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ALA B  94 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ILE B  26 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 10.702A  pdb=" N   THR B  96 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   LEU B  89 " --> pdb=" O   ILE B  77 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ILE B  77 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   MET B  91 " --> pdb=" O   GLN B  75 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ASP B  93 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   TYR B  73 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 40
      removed outlier: 6.594A  pdb=" N   ILE B  20 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   VAL B  90 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   GLU B  22 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   CYS B  92 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   ILE B  24 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ALA B  94 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ILE B  26 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 10.702A  pdb=" N   THR B  96 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 190
      removed outlier: 6.363A  pdb=" N   GLN B 201 " --> pdb=" O   SER B 187 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ILE B 189 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLU B 199 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE B 128 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   TYR B 126 " --> pdb=" O   PRO B 204 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 186 through 190
      removed outlier: 6.363A  pdb=" N   GLN B 201 " --> pdb=" O   SER B 187 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ILE B 189 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLU B 199 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE B 128 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   TYR B 126 " --> pdb=" O   PRO B 204 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 40
      removed outlier: 6.486A  pdb=" N   ILE C  20 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   VAL C  90 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   GLU C  22 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   CYS C  92 " --> pdb=" O   GLU C  22 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   ILE C  24 " --> pdb=" O   CYS C  92 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ALA C  94 " --> pdb=" O   ILE C  24 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   ILE C  26 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU C  89 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ILE C  77 " --> pdb=" O   LEU C  89 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   MET C  91 " --> pdb=" O   GLN C  75 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP C  93 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   TYR C  73 " --> pdb=" O   ASP C  93 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 191
      removed outlier: 3.948A  pdb=" N   GLY C 188 " --> pdb=" O   GLN C 201 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU C 199 " --> pdb=" O   ASN C 190 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE C 128 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 205 through 206
      removed outlier: 4.394A  pdb=" N   SER C 205 " --> pdb=" O   TYR C 126 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   TYR C 126 " --> pdb=" O   SER C 205 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 40
      removed outlier: 6.388A  pdb=" N   ILE D  20 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   VAL D  90 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   GLU D  22 " --> pdb=" O   VAL D  90 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   CYS D  92 " --> pdb=" O   GLU D  22 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   ILE D  24 " --> pdb=" O   CYS D  92 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA D  94 " --> pdb=" O   ILE D  24 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ILE D  26 " --> pdb=" O   ALA D  94 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LEU D  89 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE D  77 " --> pdb=" O   LEU D  89 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   MET D  91 " --> pdb=" O   GLN D  75 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP D  93 " --> pdb=" O   TYR D  73 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TYR D  73 " --> pdb=" O   ASP D  93 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 191
      removed outlier: 6.401A  pdb=" N   GLN D 201 " --> pdb=" O   SER D 187 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ILE D 189 " --> pdb=" O   GLU D 199 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   GLU D 199 " --> pdb=" O   ILE D 189 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN D 130 " --> pdb=" O   PHE D 200 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL D 202 " --> pdb=" O   ILE D 128 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ILE D 128 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 205 through 206
      removed outlier: 4.003A  pdb=" N   SER D 205 " --> pdb=" O   TYR D 126 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   TYR D 126 " --> pdb=" O   SER D 205 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 33 through 40
      removed outlier: 6.406A  pdb=" N   ILE E  20 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL E  90 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   GLU E  22 " --> pdb=" O   VAL E  90 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   CYS E  92 " --> pdb=" O   GLU E  22 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   ILE E  24 " --> pdb=" O   CYS E  92 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   ALA E  94 " --> pdb=" O   ILE E  24 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   ILE E  26 " --> pdb=" O   ALA E  94 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ASP E  93 " --> pdb=" O   PRO E  74 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   TYR E  95 " --> pdb=" O   LEU E  72 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   LEU E  72 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 186 through 191
      removed outlier: 6.597A  pdb=" N   GLN E 201 " --> pdb=" O   SER E 187 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   ILE E 189 " --> pdb=" O   GLU E 199 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU E 199 " --> pdb=" O   ILE E 189 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE E 128 " --> pdb=" O   VAL E 202 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 186 through 191
      removed outlier: 6.597A  pdb=" N   GLN E 201 " --> pdb=" O   SER E 187 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   ILE E 189 " --> pdb=" O   GLU E 199 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU E 199 " --> pdb=" O   ILE E 189 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE E 128 " --> pdb=" O   VAL E 202 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1125 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: 1.32

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2824
        1.34 -     1.45: 1465
        1.45 -     1.57: 5096
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 9475
  Sorted by residual:
  bond pdb=" CG  LEU C  33 "
       pdb=" CD2 LEU C  33 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.03e+00
  bond pdb=" CG1 ILE C  24 "
       pdb=" CD1 ILE C  24 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.32e+00
  bond pdb=" CA  ALA A 348 "
       pdb=" C   ALA A 348 "
    ideal  model  delta    sigma   weight residual
    1.527  1.512  0.015 1.41e-02 5.03e+03 1.13e+00
  bond pdb=" N   ILE A 347 "
       pdb=" CA  ILE A 347 "
    ideal  model  delta    sigma   weight residual
    1.458  1.472 -0.015 1.41e-02 5.03e+03 1.08e+00
  bond pdb=" N   ASN A 349 "
       pdb=" CA  ASN A 349 "
    ideal  model  delta    sigma   weight residual
    1.459  1.470 -0.011 1.15e-02 7.56e+03 8.84e-01
  ... (remaining 9470 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 12452
        1.71 -     3.42: 368
        3.42 -     5.12: 36
        5.12 -     6.83: 7
        6.83 -     8.54: 2
  Bond angle restraints: 12865
  Sorted by residual:
  angle pdb=" N   GLY D 188 "
        pdb=" CA  GLY D 188 "
        pdb=" C   GLY D 188 "
      ideal   model   delta    sigma   weight residual
     111.37  115.11   -3.74 1.29e+00 6.01e-01 8.42e+00
  angle pdb=" N   GLY B 188 "
        pdb=" CA  GLY B 188 "
        pdb=" C   GLY B 188 "
      ideal   model   delta    sigma   weight residual
     111.37  114.82   -3.45 1.29e+00 6.01e-01 7.17e+00
  angle pdb=" C   GLN B  52 "
        pdb=" N   TRP B  53 "
        pdb=" CA  TRP B  53 "
      ideal   model   delta    sigma   weight residual
     122.20  117.74    4.46 1.72e+00 3.38e-01 6.73e+00
  angle pdb=" CA  MET C 194 "
        pdb=" CB  MET C 194 "
        pdb=" CG  MET C 194 "
      ideal   model   delta    sigma   weight residual
     114.10  119.09   -4.99 2.00e+00 2.50e-01 6.22e+00
  angle pdb=" CA  LEU B  72 "
        pdb=" CB  LEU B  72 "
        pdb=" CG  LEU B  72 "
      ideal   model   delta    sigma   weight residual
     116.30  124.84   -8.54 3.50e+00 8.16e-02 5.95e+00
  ... (remaining 12860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5115
       17.99 -    35.98: 443
       35.98 -    53.96: 57
       53.96 -    71.95: 17
       71.95 -    89.94: 8
  Dihedral angle restraints: 5640
    sinusoidal: 2215
      harmonic: 3425
  Sorted by residual:
  dihedral pdb=" CA  ARG A  83 "
           pdb=" C   ARG A  83 "
           pdb=" N   ARG A  84 "
           pdb=" CA  ARG A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.77  -20.23     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ARG D  83 "
           pdb=" C   ARG D  83 "
           pdb=" N   ARG D  84 "
           pdb=" CA  ARG D  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.28  -19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  LYS A  36 "
           pdb=" C   LYS A  36 "
           pdb=" N   ALA A  37 "
           pdb=" CA  ALA A  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.06  -16.94     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 5637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 896
       0.039 -    0.077: 377
       0.077 -    0.116: 92
       0.116 -    0.154: 26
       0.154 -    0.193: 4
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CB  ILE C  24 "
            pdb=" CA  ILE C  24 "
            pdb=" CG1 ILE C  24 "
            pdb=" CG2 ILE C  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" CA  ILE B  24 "
            pdb=" N   ILE B  24 "
            pdb=" C   ILE B  24 "
            pdb=" CB  ILE B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CA  ILE A  24 "
            pdb=" N   ILE A  24 "
            pdb=" C   ILE A  24 "
            pdb=" CB  ILE A  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.91e-01
  ... (remaining 1392 not shown)

  Planarity restraints: 1665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  53 "   -0.020 2.00e-02 2.50e+03   1.48e-02 5.45e+00
        pdb=" CG  TRP D  53 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  53 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  53 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  53 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  53 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  53 "    0.019 2.00e-02 2.50e+03   1.44e-02 5.17e+00
        pdb=" CG  TRP B  53 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  53 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  53 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  53 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  53 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 102 "    0.037 5.00e-02 4.00e+02   5.66e-02 5.13e+00
        pdb=" N   PRO C 103 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 103 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 103 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1662 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 204
        2.67 -     3.23: 9344
        3.23 -     3.78: 14518
        3.78 -     4.34: 18997
        4.34 -     4.90: 31129
  Nonbonded interactions: 74192
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 130 "
            pdb=" NH1 ARG B 218 "
     model   vdw
     2.111 3.120
  nonbonded pdb=" OG1 THR C  39 "
            pdb=" OH  TYR D 176 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OG1 THR D  39 "
            pdb=" OH  TYR E 176 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   TYR B  23 "
            pdb=" OG  SER B  35 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG  SER C 205 "
            pdb=" OG  SER C 209 "
     model   vdw
     2.198 3.040
  ... (remaining 74187 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.090
  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:          0.340
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.820
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6255
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      :  0.004   0.047   9475  Z= 0.169
  Angle     :  0.661   8.538  12865  Z= 0.361
  Chirality :  0.046   0.193   1395
  Planarity :  0.006   0.065   1665
  Dihedral  : 13.728  89.938   3450
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.50 %
    Favored  : 99.21 %
  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: -0.94 (0.24), residues: 1145
  helix: -0.30 (0.28), residues: 310
  sheet: -0.80 (0.27), residues: 340
  loop : -0.49 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  83 
 TYR   0.024   0.002   TYR C 176 
 PHE   0.017   0.002   PHE C 200 
 TRP   0.040   0.002   TRP D  53 
 HIS   0.004   0.001   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 9475)
  covalent geometry    : angle       0.66096 (12865)
  hydrogen bonds       : bond        0.22814 (  388)
  hydrogen bonds       : angle       8.57750 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 173
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7151 (mtp180)
REVERT: A   52 GLN cc_start: 0.7544 (mp10) cc_final: 0.7311 (mp10)
REVERT: A  189 ILE cc_start: 0.8773 (pt) cc_final: 0.8441 (pt)
REVERT: B   38 ARG cc_start: 0.7635 (ttt180) cc_final: 0.7163 (mtp180)
REVERT: B   52 GLN cc_start: 0.6835 (tp-100) cc_final: 0.6454 (tm-30)
REVERT: B  189 ILE cc_start: 0.8519 (pt) cc_final: 0.8228 (pt)
REVERT: C   11 ASN cc_start: 0.8054 (t0) cc_final: 0.7723 (t0)
REVERT: C   38 ARG cc_start: 0.7525 (ttt180) cc_final: 0.6823 (mtp180)
REVERT: C   52 GLN cc_start: 0.7621 (mp10) cc_final: 0.7330 (mp10)
REVERT: D   38 ARG cc_start: 0.7406 (ttt180) cc_final: 0.6799 (mtp180)
REVERT: D   52 GLN cc_start: 0.7563 (mp10) cc_final: 0.7276 (mp10)
REVERT: E   11 ASN cc_start: 0.8005 (t0) cc_final: 0.7695 (t0)
REVERT: E   38 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7017 (mtp180)
REVERT: E   52 GLN cc_start: 0.7526 (mp10) cc_final: 0.7283 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0814
  time to fit residues: 20.8754
Evaluate side-chains
  145 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 249 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5008 r_free = 0.5008 target = 0.224046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.159503 restraints weight = 11891.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.165718 restraints weight = 7719.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.169701 restraints weight = 5992.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.172248 restraints weight = 5133.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.173731 restraints weight = 4660.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6263
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9475  Z= 0.145
  Angle     :  0.603   7.646  12865  Z= 0.322
  Chirality :  0.046   0.158   1395
  Planarity :  0.005   0.057   1665
  Dihedral  :  4.597  18.524   1280
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.32 %
    Favored  : 90.20 %
  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: -0.31 (0.25), residues: 1145
  helix:  0.64 (0.27), residues: 315
  sheet: -0.55 (0.27), residues: 340
  loop : -0.34 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  83 
 TYR   0.021   0.002   TYR E  55 
 PHE   0.020   0.002   PHE C 200 
 TRP   0.022   0.002   TRP A  53 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9475)
  covalent geometry    : angle       0.60268 (12865)
  hydrogen bonds       : bond        0.04632 (  388)
  hydrogen bonds       : angle       5.61473 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7655 (mp10) cc_final: 0.7387 (mp10)
REVERT: A   53 TRP cc_start: 0.7175 (t60) cc_final: 0.6957 (t60)
REVERT: A  199 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7282 (mp0)
REVERT: B  189 ILE cc_start: 0.8671 (pt) cc_final: 0.8354 (pt)
REVERT: E   11 ASN cc_start: 0.7922 (t0) cc_final: 0.7642 (t0)
REVERT: E  201 GLN cc_start: 0.7824 (mp-120) cc_final: 0.6986 (mp-120)
  outliers start: 15
  outliers final: 11
  residues processed: 163
  average time/residue: 0.0674
  time to fit residues: 16.7276
Evaluate side-chains
  147 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue  199 GLU
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 73 optimal weight:    0.1980
   chunk 24 optimal weight:    6.9990
   chunk 4 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0670
   chunk 32 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0070
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5038 r_free = 0.5038 target = 0.227222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.162840 restraints weight = 11954.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.168933 restraints weight = 7846.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.172843 restraints weight = 6123.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.175286 restraints weight = 5267.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.176896 restraints weight = 4802.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.4525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6183
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9475  Z= 0.108
  Angle     :  0.549   8.284  12865  Z= 0.287
  Chirality :  0.045   0.200   1395
  Planarity :  0.005   0.056   1665
  Dihedral  :  4.291  16.775   1280
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.70 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.25), residues: 1145
  helix:  1.13 (0.27), residues: 315
  sheet: -0.33 (0.28), residues: 350
  loop :  0.07 (0.31), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  83 
 TYR   0.015   0.001   TYR E  55 
 PHE   0.016   0.001   PHE C 200 
 TRP   0.020   0.001   TRP D  53 
 HIS   0.003   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9475)
  covalent geometry    : angle       0.54908 (12865)
  hydrogen bonds       : bond        0.03636 (  388)
  hydrogen bonds       : angle       4.98359 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7591 (mp10) cc_final: 0.7273 (mp10)
REVERT: B   50 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7844 (mp)
REVERT: B  189 ILE cc_start: 0.8615 (pt) cc_final: 0.8337 (pt)
REVERT: C   52 GLN cc_start: 0.7542 (mp10) cc_final: 0.7276 (mp10)
REVERT: E   11 ASN cc_start: 0.7856 (t0) cc_final: 0.7615 (t0)
REVERT: E   52 GLN cc_start: 0.7657 (mp10) cc_final: 0.7410 (mp10)
REVERT: E  173 ASP cc_start: 0.7178 (m-30) cc_final: 0.6956 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 178
  average time/residue: 0.0707
  time to fit residues: 19.2167
Evaluate side-chains
  164 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  170 ASP
Chi-restraints excluded: chain E residue  172 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 112 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 ASN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.214965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.148649 restraints weight = 12221.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.154091 restraints weight = 8158.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.157471 restraints weight = 6475.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.159621 restraints weight = 5652.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.160597 restraints weight = 5206.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6442
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9475  Z= 0.218
  Angle     :  0.688   9.475  12865  Z= 0.365
  Chirality :  0.049   0.179   1395
  Planarity :  0.005   0.056   1665
  Dihedral  :  4.966  19.796   1280
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.66 %
    Favored  : 83.96 %
  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: -0.52 (0.25), residues: 1145
  helix:  0.50 (0.27), residues: 315
  sheet: -1.05 (0.25), residues: 410
  loop :  0.07 (0.34), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 218 
 TYR   0.020   0.002   TYR A 132 
 PHE   0.018   0.002   PHE B 200 
 TRP   0.028   0.002   TRP D  53 
 HIS   0.006   0.002   HIS C 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 9475)
  covalent geometry    : angle       0.68797 (12865)
  hydrogen bonds       : bond        0.05208 (  388)
  hydrogen bonds       : angle       5.69285 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   52 GLN cc_start: 0.7906 (mp10) cc_final: 0.7607 (mp10)
REVERT: A  201 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7303 (mm110)
REVERT: B   50 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7837 (mp)
REVERT: B   52 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7280 (tm-30)
REVERT: B  189 ILE cc_start: 0.8765 (pt) cc_final: 0.8365 (pt)
REVERT: C   31 MET cc_start: 0.7179 (mtt) cc_final: 0.5520 (tmm)
REVERT: C   52 GLN cc_start: 0.7902 (mp10) cc_final: 0.7582 (mp10)
REVERT: C   83 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7569 (mtt180)
REVERT: D   11 ASN cc_start: 0.8076 (t0) cc_final: 0.7817 (t0)
REVERT: D   32 ASP cc_start: 0.6261 (m-30) cc_final: 0.5824 (m-30)
REVERT: D  201 GLN cc_start: 0.7784 (mm110) cc_final: 0.7570 (mm110)
REVERT: E   11 ASN cc_start: 0.8104 (t0) cc_final: 0.7824 (t0)
REVERT: E   19 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6979 (mm)
REVERT: E  170 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7282 (t0)
REVERT: E  173 ASP cc_start: 0.7361 (m-30) cc_final: 0.7018 (m-30)
REVERT: E  201 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7488 (mm-40)
  outliers start: 24
  outliers final: 14
  residues processed: 155
  average time/residue: 0.0671
  time to fit residues: 16.3136
Evaluate side-chains
  150 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  170 ASP
Chi-restraints excluded: chain E residue  172 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 89 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 71 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.222926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.158645 restraints weight = 12188.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.164214 restraints weight = 8277.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.167642 restraints weight = 6595.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.169302 restraints weight = 5753.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.171062 restraints weight = 5333.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9475  Z= 0.114
  Angle     :  0.557   7.148  12865  Z= 0.293
  Chirality :  0.045   0.156   1395
  Planarity :  0.005   0.055   1665
  Dihedral  :  4.420  16.860   1280
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.35 %
    Favored  : 82.87 %
  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: -0.05 (0.26), residues: 1145
  helix:  1.08 (0.27), residues: 315
  sheet: -0.93 (0.25), residues: 410
  loop :  0.36 (0.34), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 218 
 TYR   0.012   0.001   TYR E  55 
 PHE   0.014   0.001   PHE C 200 
 TRP   0.024   0.001   TRP D  53 
 HIS   0.003   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9475)
  covalent geometry    : angle       0.55737 (12865)
  hydrogen bonds       : bond        0.03594 (  388)
  hydrogen bonds       : angle       4.90360 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7718 (mp10) cc_final: 0.7392 (mp10)
REVERT: A  201 GLN cc_start: 0.7824 (mm110) cc_final: 0.7454 (mm-40)
REVERT: B   50 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7778 (mp)
REVERT: B   52 GLN cc_start: 0.7473 (tp-100) cc_final: 0.7083 (tm-30)
REVERT: B  189 ILE cc_start: 0.8703 (pt) cc_final: 0.8360 (pt)
REVERT: C   31 MET cc_start: 0.7144 (mtt) cc_final: 0.5596 (tmm)
REVERT: D   11 ASN cc_start: 0.7928 (t0) cc_final: 0.7671 (t0)
REVERT: D  201 GLN cc_start: 0.7636 (mm110) cc_final: 0.7369 (mm110)
REVERT: E   11 ASN cc_start: 0.7911 (t0) cc_final: 0.7680 (t0)
REVERT: E   52 GLN cc_start: 0.7671 (mp10) cc_final: 0.7470 (mp10)
REVERT: E  173 ASP cc_start: 0.7218 (m-30) cc_final: 0.6884 (m-30)
REVERT: E  201 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7220 (mm-40)
  outliers start: 18
  outliers final: 13
  residues processed: 159
  average time/residue: 0.0662
  time to fit residues: 16.3609
Evaluate side-chains
  153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  170 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0570
   chunk 82 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.8104

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.217295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.151645 restraints weight = 12161.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.157202 restraints weight = 8003.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.160748 restraints weight = 6279.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.162325 restraints weight = 5425.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.164217 restraints weight = 5021.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6364
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9475  Z= 0.166
  Angle     :  0.615   7.826  12865  Z= 0.323
  Chirality :  0.046   0.168   1395
  Planarity :  0.005   0.055   1665
  Dihedral  :  4.644  17.948   1280
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.23 %
    Favored  : 80.50 %
  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: -0.40 (0.25), residues: 1145
  helix:  0.68 (0.27), residues: 320
  sheet: -1.02 (0.25), residues: 410
  loop :  0.10 (0.34), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 218 
 TYR   0.017   0.002   TYR E  55 
 PHE   0.016   0.002   PHE C 200 
 TRP   0.025   0.002   TRP D  53 
 HIS   0.003   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9475)
  covalent geometry    : angle       0.61480 (12865)
  hydrogen bonds       : bond        0.04309 (  388)
  hydrogen bonds       : angle       5.23261 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   52 GLN cc_start: 0.7869 (mp10) cc_final: 0.7531 (mp10)
REVERT: A  201 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7534 (mm-40)
REVERT: B   50 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: B  189 ILE cc_start: 0.8772 (pt) cc_final: 0.8400 (pt)
REVERT: C   31 MET cc_start: 0.7173 (mtt) cc_final: 0.5732 (tmm)
REVERT: C   52 GLN cc_start: 0.7854 (mp10) cc_final: 0.7621 (mp10)
REVERT: C   83 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7532 (mtt180)
REVERT: D   11 ASN cc_start: 0.8126 (t0) cc_final: 0.7816 (t0)
REVERT: D   32 ASP cc_start: 0.6315 (m-30) cc_final: 0.5841 (m-30)
REVERT: D  201 GLN cc_start: 0.7806 (mm110) cc_final: 0.7601 (mm110)
REVERT: E   11 ASN cc_start: 0.8143 (t0) cc_final: 0.7861 (t0)
REVERT: E   19 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.6989 (mm)
REVERT: E  170 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7231 (t0)
REVERT: E  173 ASP cc_start: 0.7424 (m-30) cc_final: 0.6956 (m-30)
REVERT: E  201 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7306 (mm-40)
  outliers start: 23
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0663
  time to fit residues: 15.8552
Evaluate side-chains
  156 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  254 THR
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  170 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.220957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.156224 restraints weight = 12887.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.161715 restraints weight = 8791.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.165208 restraints weight = 7042.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.167510 restraints weight = 6164.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.168920 restraints weight = 5667.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9475  Z= 0.126
  Angle     :  0.569   6.507  12865  Z= 0.299
  Chirality :  0.045   0.164   1395
  Planarity :  0.004   0.054   1665
  Dihedral  :  4.413  17.474   1280
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.61 %
    Favored  : 78.81 %
  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: -0.20 (0.25), residues: 1145
  helix:  0.87 (0.27), residues: 315
  sheet: -0.96 (0.25), residues: 410
  loop :  0.28 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 218 
 TYR   0.014   0.001   TYR E  55 
 PHE   0.014   0.002   PHE C 200 
 TRP   0.023   0.001   TRP D  53 
 HIS   0.003   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9475)
  covalent geometry    : angle       0.56918 (12865)
  hydrogen bonds       : bond        0.03708 (  388)
  hydrogen bonds       : angle       4.90166 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   52 GLN cc_start: 0.7769 (mp10) cc_final: 0.7446 (mp10)
REVERT: A  201 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7502 (mm-40)
REVERT: B   50 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7694 (mp)
REVERT: B  189 ILE cc_start: 0.8778 (pt) cc_final: 0.8408 (pt)
REVERT: C   31 MET cc_start: 0.7178 (mtt) cc_final: 0.5788 (tmm)
REVERT: C   52 GLN cc_start: 0.7777 (mp10) cc_final: 0.7518 (mp10)
REVERT: D   11 ASN cc_start: 0.7991 (t0) cc_final: 0.7694 (t0)
REVERT: D   75 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7765 (mm-40)
REVERT: D  201 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7463 (mm-40)
REVERT: E   11 ASN cc_start: 0.8018 (t0) cc_final: 0.7797 (t0)
REVERT: E   19 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7155 (mm)
REVERT: E  173 ASP cc_start: 0.7326 (m-30) cc_final: 0.6901 (m-30)
REVERT: E  201 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7219 (mm-40)
  outliers start: 26
  outliers final: 21
  residues processed: 151
  average time/residue: 0.0680
  time to fit residues: 16.2541
Evaluate side-chains
  159 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  201 GLN
Chi-restraints excluded: chain D residue  254 THR
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  170 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 70 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 197 GLN
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.219796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.154386 restraints weight = 12819.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.160070 restraints weight = 8707.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.163569 restraints weight = 6946.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.165806 restraints weight = 6073.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.167181 restraints weight = 5584.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6384
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9475  Z= 0.124
  Angle     :  0.571   8.682  12865  Z= 0.296
  Chirality :  0.045   0.160   1395
  Planarity :  0.004   0.054   1665
  Dihedral  :  4.391  17.188   1280
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.71 %
    Favored  : 78.51 %
  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: -0.15 (0.25), residues: 1145
  helix:  0.94 (0.27), residues: 315
  sheet: -0.97 (0.25), residues: 410
  loop :  0.33 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 218 
 TYR   0.016   0.001   TYR B  55 
 PHE   0.014   0.002   PHE C 200 
 TRP   0.024   0.001   TRP D  53 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9475)
  covalent geometry    : angle       0.57080 (12865)
  hydrogen bonds       : bond        0.03635 (  388)
  hydrogen bonds       : angle       4.83772 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7777 (mp10) cc_final: 0.7441 (mp10)
REVERT: A  201 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7526 (mm-40)
REVERT: B   50 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7716 (mp)
REVERT: B  189 ILE cc_start: 0.8744 (pt) cc_final: 0.8340 (pt)
REVERT: C   31 MET cc_start: 0.7190 (mtt) cc_final: 0.5832 (tmm)
REVERT: C   52 GLN cc_start: 0.7762 (mp10) cc_final: 0.7477 (mp10)
REVERT: D   11 ASN cc_start: 0.8023 (t0) cc_final: 0.7712 (t0)
REVERT: D   75 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7791 (mm-40)
REVERT: D  201 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7451 (mm-40)
REVERT: E   11 ASN cc_start: 0.8051 (t0) cc_final: 0.7827 (t0)
REVERT: E   19 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7143 (mm)
REVERT: E  173 ASP cc_start: 0.7375 (m-30) cc_final: 0.6939 (m-30)
REVERT: E  197 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7710 (pp30)
REVERT: E  201 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7217 (mm-40)
  outliers start: 28
  outliers final: 19
  residues processed: 148
  average time/residue: 0.0711
  time to fit residues: 16.1985
Evaluate side-chains
  157 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  201 GLN
Chi-restraints excluded: chain D residue  254 THR
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue  170 ASP
Chi-restraints excluded: chain E residue  197 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0270
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0010
   chunk 41 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   chunk 45 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.7846

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 ASN
D 130 GLN
D 190 ASN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.221510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.155785 restraints weight = 12672.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.161598 restraints weight = 8532.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.165164 restraints weight = 6781.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.167446 restraints weight = 5912.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.168892 restraints weight = 5425.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9475  Z= 0.115
  Angle     :  0.561   8.160  12865  Z= 0.290
  Chirality :  0.044   0.164   1395
  Planarity :  0.005   0.053   1665
  Dihedral  :  4.308  17.273   1280
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.71 %
    Favored  : 78.51 %
  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: -0.04 (0.25), residues: 1145
  helix:  1.04 (0.27), residues: 315
  sheet: -0.95 (0.25), residues: 410
  loop :  0.44 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  83 
 TYR   0.023   0.001   TYR E  55 
 PHE   0.013   0.001   PHE C 200 
 TRP   0.021   0.001   TRP D  53 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9475)
  covalent geometry    : angle       0.56073 (12865)
  hydrogen bonds       : bond        0.03457 (  388)
  hydrogen bonds       : angle       4.71154 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7212 (pt)
REVERT: A   52 GLN cc_start: 0.7732 (mp10) cc_final: 0.7388 (mp10)
REVERT: A  201 GLN cc_start: 0.7944 (mm110) cc_final: 0.7544 (mm-40)
REVERT: B   50 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7730 (mp)
REVERT: B  189 ILE cc_start: 0.8679 (pt) cc_final: 0.8334 (pt)
REVERT: C   31 MET cc_start: 0.7166 (mtt) cc_final: 0.5842 (tmm)
REVERT: C   52 GLN cc_start: 0.7728 (mp10) cc_final: 0.7420 (mp10)
REVERT: D   11 ASN cc_start: 0.8042 (t0) cc_final: 0.7721 (t0)
REVERT: D  201 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7324 (mm-40)
REVERT: E   11 ASN cc_start: 0.8061 (t0) cc_final: 0.7849 (t0)
REVERT: E  173 ASP cc_start: 0.7410 (m-30) cc_final: 0.7001 (m-30)
REVERT: E  201 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7233 (mm-40)
  outliers start: 28
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0705
  time to fit residues: 17.1298
Evaluate side-chains
  160 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  190 ASN
Chi-restraints excluded: chain D residue  201 GLN
Chi-restraints excluded: chain D residue  254 THR
Chi-restraints excluded: chain E residue   24 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  170 ASP
Chi-restraints excluded: chain E residue  172 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0870
   chunk 30 optimal weight:    0.0870
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0170
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 94 optimal weight:    0.1980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 190 ASN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.220966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.155356 restraints weight = 12585.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.161116 restraints weight = 8476.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.164831 restraints weight = 6717.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.167042 restraints weight = 5831.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.168096 restraints weight = 5350.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6320
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   9475  Z= 0.146
  Angle     :  0.873  59.200  12865  Z= 0.499
  Chirality :  0.046   0.364   1395
  Planarity :  0.005   0.053   1665
  Dihedral  :  4.367  23.969   1280
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.01 %
    Favored  : 78.32 %
  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: -0.02 (0.25), residues: 1145
  helix:  1.04 (0.27), residues: 315
  sheet: -0.94 (0.25), residues: 410
  loop :  0.46 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 218 
 TYR   0.023   0.001   TYR A 176 
 PHE   0.017   0.002   PHE E 200 
 TRP   0.021   0.001   TRP D  53 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9475)
  covalent geometry    : angle       0.87252 (12865)
  hydrogen bonds       : bond        0.03441 (  388)
  hydrogen bonds       : angle       4.70545 ( 1125)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7179 (pt)
REVERT: A   52 GLN cc_start: 0.7735 (mp10) cc_final: 0.7383 (mp10)
REVERT: A  201 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7537 (mm-40)
REVERT: B   50 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7727 (mp)
REVERT: B  189 ILE cc_start: 0.8676 (pt) cc_final: 0.8324 (pt)
REVERT: C   31 MET cc_start: 0.7175 (mtt) cc_final: 0.5835 (tmm)
REVERT: C   52 GLN cc_start: 0.7731 (mp10) cc_final: 0.7416 (mp10)
REVERT: D   11 ASN cc_start: 0.8063 (t0) cc_final: 0.7734 (t0)
REVERT: D  201 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7333 (mm-40)
REVERT: E   11 ASN cc_start: 0.8077 (t0) cc_final: 0.7867 (t0)
REVERT: E   19 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7002 (mm)
REVERT: E  173 ASP cc_start: 0.7440 (m-30) cc_final: 0.7017 (m-30)
REVERT: E  201 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7224 (mm-40)
  outliers start: 27
  outliers final: 21
  residues processed: 151
  average time/residue: 0.0616
  time to fit residues: 14.7317
Evaluate side-chains
  163 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain A residue   53 TRP
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  130 GLN
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  201 GLN
Chi-restraints excluded: chain D residue  254 THR
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   24 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  170 ASP
Chi-restraints excluded: chain E residue  172 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0980
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.221122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.155537 restraints weight = 12547.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.161197 restraints weight = 8484.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.164867 restraints weight = 6738.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.167143 restraints weight = 5865.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.168515 restraints weight = 5398.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   9475  Z= 0.146
  Angle     :  0.873  59.200  12865  Z= 0.499
  Chirality :  0.046   0.364   1395
  Planarity :  0.005   0.053   1665
  Dihedral  :  4.367  23.969   1280
  Min Nonbonded Distance : 1.644

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.11 %
    Favored  : 78.32 %
  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: -0.02 (0.25), residues: 1145
  helix:  1.04 (0.27), residues: 315
  sheet: -0.94 (0.25), residues: 410
  loop :  0.46 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 218 
 TYR   0.023   0.001   TYR A 176 
 PHE   0.017   0.002   PHE E 200 
 TRP   0.021   0.001   TRP D  53 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9475)
  covalent geometry    : angle       0.87252 (12865)
  hydrogen bonds       : bond        0.03441 (  388)
  hydrogen bonds       : angle       4.70545 ( 1125)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1897.31 seconds
wall clock time: 33 minutes 27.79 seconds (2007.79 seconds total)