Starting phenix.real_space_refine
on Sun Jun  8 05:38:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v4k_31714/06_2025/7v4k_31714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v4k_31714/06_2025/7v4k_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v4k_31714/06_2025/7v4k_31714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v4k_31714/06_2025/7v4k_31714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v4k_31714/06_2025/7v4k_31714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v4k_31714/06_2025/7v4k_31714.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.00, per 1000 atoms: 0.86
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.19
  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: 2.66

  Time building geometry restraints manager: 2.98 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: 0.02
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:             15.670
  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:          0.470
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.360
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.100
-------------------------------------------------------------------------------
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 : 17.66
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (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
 TRP   0.040   0.002   TRP D  53 
 HIS   0.004   0.001   HIS B 175 
 PHE   0.017   0.002   PHE C 200 
 TYR   0.024   0.002   TYR C 176 
 ARG   0.007   0.001   ARG A  83 

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

*********************** 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  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7152 (mtp180)
REVERT: A   52 GLN cc_start: 0.7544 (mp10) cc_final: 0.7312 (mp10)
REVERT: A  189 ILE cc_start: 0.8773 (pt) cc_final: 0.8455 (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: 0.6455 (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: 0.7331 (mp10)
REVERT: D   38 ARG cc_start: 0.7406 (ttt180) cc_final: 0.6798 (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: 0.7694 (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: 0.1921
  time to fit residues: 48.4361
Evaluate side-chains
  144 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    0.4980
   chunk 67 optimal weight:    6.9990
   chunk 104 optimal weight:    9.9990
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.4969 r_free = 0.4969 target = 0.219904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.153694 restraints weight = 11833.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.160064 restraints weight = 7526.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.164111 restraints weight = 5791.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6320
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9475  Z= 0.177
  Angle     :  0.641   8.015  12865  Z= 0.342
  Chirality :  0.047   0.158   1395
  Planarity :  0.006   0.058   1665
  Dihedral  :  4.814  19.030   1280
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  8.51 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.25), residues: 1145
  helix:  0.45 (0.27), residues: 315
  sheet: -0.64 (0.27), residues: 340
  loop : -0.52 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D  53 
 HIS   0.004   0.001   HIS A 175 
 PHE   0.021   0.002   PHE C 200 
 TYR   0.017   0.002   TYR E  55 
 ARG   0.005   0.001   ARG E  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04789 (  388)
  hydrogen bonds       : angle       5.82963 ( 1125)
  covalent geometry    : bond        0.00411 ( 9475)
  covalent geometry    : angle       0.64089 (12865)

*********************** 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
  171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 1.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7773 (mp10) cc_final: 0.7503 (mp10)
REVERT: A  189 ILE cc_start: 0.8919 (pt) cc_final: 0.8710 (pt)
REVERT: B  189 ILE cc_start: 0.8731 (pt) cc_final: 0.8395 (pt)
REVERT: C   11 ASN cc_start: 0.8108 (t0) cc_final: 0.7863 (t0)
REVERT: C   52 GLN cc_start: 0.7892 (mp10) cc_final: 0.7525 (mp10)
REVERT: C  235 ASP cc_start: 0.6169 (p0) cc_final: 0.5934 (t70)
REVERT: D   11 ASN cc_start: 0.8055 (t0) cc_final: 0.7827 (t0)
REVERT: D  235 ASP cc_start: 0.6372 (p0) cc_final: 0.5998 (t70)
REVERT: E   11 ASN cc_start: 0.8125 (t0) cc_final: 0.7788 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 161
  average time/residue: 0.2919
  time to fit residues: 70.5934
Evaluate side-chains
  145 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 2.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  170 ASP
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  170 ASP
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 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:   20.0000
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 114 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4988 r_free = 0.4988 target = 0.221675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.156493 restraints weight = 11967.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.162175 restraints weight = 8029.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.165797 restraints weight = 6369.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.2315

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= 0.133
  Angle     :  0.571   6.900  12865  Z= 0.302
  Chirality :  0.045   0.149   1395
  Planarity :  0.005   0.058   1665
  Dihedral  :  4.546  18.072   1280
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.29 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.25), residues: 1145
  helix:  0.79 (0.27), residues: 315
  sheet: -0.59 (0.27), residues: 370
  loop : -0.12 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D  53 
 HIS   0.004   0.001   HIS A 175 
 PHE   0.017   0.002   PHE C 200 
 TYR   0.014   0.001   TYR E  55 
 ARG   0.005   0.001   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04125 (  388)
  hydrogen bonds       : angle       5.37260 ( 1125)
  covalent geometry    : bond        0.00305 ( 9475)
  covalent geometry    : angle       0.57064 (12865)

*********************** 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
  183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 1.113 
Fit side-chains
REVERT: A   52 GLN cc_start: 0.7757 (mp10) cc_final: 0.7426 (mp10)
REVERT: B   50 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7833 (mp)
REVERT: B  189 ILE cc_start: 0.8730 (pt) cc_final: 0.8389 (pt)
REVERT: C   11 ASN cc_start: 0.7982 (t0) cc_final: 0.7747 (t0)
REVERT: C   52 GLN cc_start: 0.7780 (mp10) cc_final: 0.7415 (mp10)
REVERT: C  235 ASP cc_start: 0.6213 (p0) cc_final: 0.5982 (t70)
REVERT: D   11 ASN cc_start: 0.8033 (t0) cc_final: 0.7739 (t0)
REVERT: D   32 ASP cc_start: 0.6214 (m-30) cc_final: 0.5788 (m-30)
REVERT: D  235 ASP cc_start: 0.6492 (p0) cc_final: 0.6074 (t70)
REVERT: E   11 ASN cc_start: 0.7983 (t0) cc_final: 0.7679 (t0)
REVERT: E  173 ASP cc_start: 0.7191 (m-30) cc_final: 0.6990 (m-30)
  outliers start: 24
  outliers final: 16
  residues processed: 171
  average time/residue: 0.1752
  time to fit residues: 44.5720
Evaluate side-chains
  154 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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   24 ILE
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   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   54 ASN
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  172 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 113 optimal weight:   20.0000
   chunk 63 optimal weight:    0.8980
   chunk 45 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 89 optimal weight:    4.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 ASN
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4932 r_free = 0.4932 target = 0.215897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.150503 restraints weight = 12074.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.155703 restraints weight = 8278.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.158862 restraints weight = 6658.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9475  Z= 0.187
  Angle     :  0.635   8.177  12865  Z= 0.337
  Chirality :  0.047   0.199   1395
  Planarity :  0.005   0.057   1665
  Dihedral  :  4.872  18.389   1280
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.25), residues: 1145
  helix:  0.43 (0.27), residues: 315
  sheet: -0.77 (0.27), residues: 380
  loop : -0.26 (0.32), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D  53 
 HIS   0.004   0.001   HIS E 175 
 PHE   0.018   0.002   PHE B 200 
 TYR   0.014   0.002   TYR D  73 
 ARG   0.006   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04767 (  388)
  hydrogen bonds       : angle       5.55837 ( 1125)
  covalent geometry    : bond        0.00439 ( 9475)
  covalent geometry    : angle       0.63546 (12865)

*********************** 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
  172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A   32 ASP cc_start: 0.5884 (m-30) cc_final: 0.5438 (m-30)
REVERT: A   52 GLN cc_start: 0.7827 (mp10) cc_final: 0.7540 (mp10)
REVERT: A  201 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7261 (mm110)
REVERT: B   50 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7796 (mp)
REVERT: B  189 ILE cc_start: 0.8768 (pt) cc_final: 0.8409 (pt)
REVERT: C   11 ASN cc_start: 0.8096 (t0) cc_final: 0.7850 (t0)
REVERT: C   31 MET cc_start: 0.7152 (mtt) cc_final: 0.5382 (tmm)
REVERT: C   52 GLN cc_start: 0.7958 (mp10) cc_final: 0.7591 (mp10)
REVERT: C  235 ASP cc_start: 0.6544 (p0) cc_final: 0.6025 (t70)
REVERT: D   11 ASN cc_start: 0.8150 (t0) cc_final: 0.7828 (t0)
REVERT: D   32 ASP cc_start: 0.6337 (m-30) cc_final: 0.5907 (m-30)
REVERT: D  201 GLN cc_start: 0.7766 (mm110) cc_final: 0.7517 (mm110)
REVERT: D  235 ASP cc_start: 0.6896 (p0) cc_final: 0.6224 (t70)
REVERT: E   11 ASN cc_start: 0.8106 (t0) cc_final: 0.7845 (t0)
REVERT: E   19 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7044 (mm)
REVERT: E  129 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6492 (mt-10)
REVERT: E  173 ASP cc_start: 0.7286 (m-30) cc_final: 0.6977 (m-30)
REVERT: E  201 GLN cc_start: 0.7730 (mm-40) cc_final: 0.6963 (mm-40)
  outliers start: 30
  outliers final: 21
  residues processed: 156
  average time/residue: 0.1577
  time to fit residues: 37.8856
Evaluate side-chains
  161 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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   92 CYS
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  201 GLN
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  199 GLU
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   54 ASN
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
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 59 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0570
   chunk 6 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.0702

-------------------------------------------------------------------------------
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**
** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** 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 = 0.4973 r_free = 0.4973 target = 0.220124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.154874 restraints weight = 12181.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.160365 restraints weight = 8292.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.163765 restraints weight = 6599.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9475  Z= 0.126
  Angle     :  0.561   5.945  12865  Z= 0.296
  Chirality :  0.045   0.164   1395
  Planarity :  0.005   0.056   1665
  Dihedral  :  4.518  17.528   1280
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.45 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.25), residues: 1145
  helix:  0.77 (0.27), residues: 315
  sheet: -0.73 (0.27), residues: 380
  loop : -0.12 (0.32), residues: 450

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  388)
  hydrogen bonds       : angle       5.07440 ( 1125)
  covalent geometry    : bond        0.00291 ( 9475)
  covalent geometry    : angle       0.56051 (12865)

*********************** 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
  172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7730 (mp10) cc_final: 0.7413 (mp10)
REVERT: A  201 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7207 (mm110)
REVERT: B   50 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7809 (mp)
REVERT: B  130 GLN cc_start: 0.7893 (tp40) cc_final: 0.7520 (tm-30)
REVERT: B  189 ILE cc_start: 0.8773 (pt) cc_final: 0.8459 (pt)
REVERT: C   11 ASN cc_start: 0.8066 (t0) cc_final: 0.7797 (t0)
REVERT: C   31 MET cc_start: 0.7050 (mtt) cc_final: 0.5305 (tmm)
REVERT: C   52 GLN cc_start: 0.7859 (mp10) cc_final: 0.7460 (mp10)
REVERT: C  235 ASP cc_start: 0.6597 (p0) cc_final: 0.5987 (t70)
REVERT: D   11 ASN cc_start: 0.8176 (t0) cc_final: 0.7833 (t0)
REVERT: D  201 GLN cc_start: 0.7680 (mm110) cc_final: 0.7358 (mm-40)
REVERT: D  235 ASP cc_start: 0.7134 (p0) cc_final: 0.6346 (t70)
REVERT: E   11 ASN cc_start: 0.8105 (t0) cc_final: 0.7837 (t0)
REVERT: E   19 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7048 (mm)
REVERT: E  173 ASP cc_start: 0.7253 (m-30) cc_final: 0.6886 (m-30)
REVERT: E  201 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7317 (mm-40)
  outliers start: 26
  outliers final: 17
  residues processed: 158
  average time/residue: 0.1669
  time to fit residues: 40.4227
Evaluate side-chains
  152 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
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 B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue  170 ASP
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 C residue  170 ASP
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  201 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 114 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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
C 190 ASN
** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.214171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.148836 restraints weight = 12478.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.154711 restraints weight = 8144.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.158428 restraints weight = 6366.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.3307

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= 0.177
  Angle     :  0.619   7.631  12865  Z= 0.328
  Chirality :  0.046   0.176   1395
  Planarity :  0.005   0.055   1665
  Dihedral  :  4.814  18.676   1280
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 16.44 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1145
  helix:  0.46 (0.27), residues: 320
  sheet: -0.87 (0.27), residues: 380
  loop : -0.38 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D  53 
 HIS   0.003   0.001   HIS E 175 
 PHE   0.016   0.002   PHE C 200 
 TYR   0.014   0.002   TYR A 132 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  388)
  hydrogen bonds       : angle       5.33540 ( 1125)
  covalent geometry    : bond        0.00420 ( 9475)
  covalent geometry    : angle       0.61946 (12865)

*********************** 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
  179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   32 ASP cc_start: 0.5927 (m-30) cc_final: 0.5448 (m-30)
REVERT: A   52 GLN cc_start: 0.7836 (mp10) cc_final: 0.7525 (mp10)
REVERT: A  201 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7292 (mm110)
REVERT: A  230 VAL cc_start: 0.7632 (m) cc_final: 0.7427 (p)
REVERT: B   50 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7851 (mp)
REVERT: B   73 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7412 (t80)
REVERT: B  130 GLN cc_start: 0.8010 (tp40) cc_final: 0.7594 (tm-30)
REVERT: B  189 ILE cc_start: 0.8779 (pt) cc_final: 0.8410 (pt)
REVERT: B  201 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7115 (mp10)
REVERT: C   11 ASN cc_start: 0.8180 (t0) cc_final: 0.7900 (t0)
REVERT: C   31 MET cc_start: 0.7104 (mtt) cc_final: 0.5476 (tmm)
REVERT: C   52 GLN cc_start: 0.8000 (mp10) cc_final: 0.7591 (mp10)
REVERT: C  235 ASP cc_start: 0.6789 (p0) cc_final: 0.6046 (t70)
REVERT: D   11 ASN cc_start: 0.8201 (t0) cc_final: 0.7878 (t0)
REVERT: D   32 ASP cc_start: 0.6412 (m-30) cc_final: 0.5955 (m-30)
REVERT: D  201 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7459 (mm-40)
REVERT: D  235 ASP cc_start: 0.7402 (p0) cc_final: 0.6499 (t70)
REVERT: E   11 ASN cc_start: 0.8209 (t0) cc_final: 0.7922 (t0)
REVERT: E   19 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7035 (mm)
REVERT: E  129 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6697 (mt-10)
REVERT: E  173 ASP cc_start: 0.7405 (m-30) cc_final: 0.6948 (m-30)
REVERT: E  201 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7145 (mm-40)
  outliers start: 40
  outliers final: 22
  residues processed: 160
  average time/residue: 0.1613
  time to fit residues: 39.0064
Evaluate side-chains
  161 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
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 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   73 TYR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   53 TRP
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  190 ASN
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   54 ASN
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   53 TRP
Chi-restraints excluded: chain E residue   54 ASN
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  201 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 78 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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**
** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 190 ASN
** E  87 ASN ** 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 = 0.4973 r_free = 0.4973 target = 0.218851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.153057 restraints weight = 12212.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.158455 restraints weight = 8318.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.161794 restraints weight = 6653.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9475  Z= 0.138
  Angle     :  0.581   6.946  12865  Z= 0.305
  Chirality :  0.045   0.155   1395
  Planarity :  0.005   0.055   1665
  Dihedral  :  4.643  18.186   1280
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.12 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.25), residues: 1145
  helix:  0.67 (0.27), residues: 315
  sheet: -0.96 (0.26), residues: 380
  loop : -0.18 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  53 
 HIS   0.004   0.001   HIS A 175 
 PHE   0.015   0.002   PHE B 200 
 TYR   0.018   0.002   TYR E  55 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  388)
  hydrogen bonds       : angle       5.02405 ( 1125)
  covalent geometry    : bond        0.00324 ( 9475)
  covalent geometry    : angle       0.58050 (12865)

*********************** 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
  169 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7717 (mp10) cc_final: 0.7420 (mp10)
REVERT: A  201 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7178 (mm110)
REVERT: B   50 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7789 (mp)
REVERT: B   52 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7256 (mp10)
REVERT: B   73 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7132 (t80)
REVERT: B  130 GLN cc_start: 0.7913 (tp40) cc_final: 0.7549 (tm-30)
REVERT: B  189 ILE cc_start: 0.8782 (pt) cc_final: 0.8456 (pt)
REVERT: C   11 ASN cc_start: 0.8062 (t0) cc_final: 0.7816 (t0)
REVERT: C   31 MET cc_start: 0.7090 (mtt) cc_final: 0.5541 (tmm)
REVERT: C   52 GLN cc_start: 0.7902 (mp10) cc_final: 0.7482 (mp10)
REVERT: C  235 ASP cc_start: 0.6791 (p0) cc_final: 0.6012 (t70)
REVERT: D   11 ASN cc_start: 0.8114 (t0) cc_final: 0.7815 (t0)
REVERT: D  235 ASP cc_start: 0.7480 (p0) cc_final: 0.6585 (t70)
REVERT: E   11 ASN cc_start: 0.8035 (t0) cc_final: 0.7796 (t0)
REVERT: E   19 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7125 (mm)
REVERT: E  173 ASP cc_start: 0.7291 (m-30) cc_final: 0.6817 (m-30)
REVERT: E  189 ILE cc_start: 0.8630 (pt) cc_final: 0.8394 (pt)
REVERT: E  201 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7282 (mm-40)
  outliers start: 30
  outliers final: 21
  residues processed: 156
  average time/residue: 0.1556
  time to fit residues: 36.8654
Evaluate side-chains
  159 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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 B residue   50 LEU
Chi-restraints excluded: chain B residue   52 GLN
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   73 TYR
Chi-restraints excluded: chain B residue  170 ASP
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   55 TYR
Chi-restraints excluded: chain C residue   92 CYS
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   54 ASN
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  254 THR
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  201 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0770
   chunk 82 optimal weight:    6.9990
   chunk 113 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.5142

-------------------------------------------------------------------------------
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**
D 190 ASN
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** 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 = 0.4957 r_free = 0.4957 target = 0.217089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.151283 restraints weight = 12433.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.156773 restraints weight = 8392.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.160287 restraints weight = 6665.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6459
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      :  0.004   0.048   9475  Z= 0.150
  Angle     :  0.593   9.039  12865  Z= 0.309
  Chirality :  0.045   0.174   1395
  Planarity :  0.005   0.054   1665
  Dihedral  :  4.672  18.052   1280
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.61 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.25), residues: 1145
  helix:  0.63 (0.27), residues: 315
  sheet: -1.00 (0.26), residues: 380
  loop : -0.13 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  53 
 HIS   0.003   0.001   HIS A 175 
 PHE   0.015   0.002   PHE B 200 
 TYR   0.022   0.002   TYR E  55 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  388)
  hydrogen bonds       : angle       5.11136 ( 1125)
  covalent geometry    : bond        0.00356 ( 9475)
  covalent geometry    : angle       0.59252 (12865)

*********************** 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
  164 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7744 (mp10) cc_final: 0.7430 (mp10)
REVERT: A  201 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7187 (mm110)
REVERT: B   50 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7824 (mp)
REVERT: B   52 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7237 (mp10)
REVERT: B   73 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7140 (t80)
REVERT: B  130 GLN cc_start: 0.7951 (tp40) cc_final: 0.7573 (tm-30)
REVERT: B  189 ILE cc_start: 0.8793 (pt) cc_final: 0.8489 (pt)
REVERT: C   11 ASN cc_start: 0.8130 (t0) cc_final: 0.7873 (t0)
REVERT: C   31 MET cc_start: 0.7203 (mtt) cc_final: 0.5850 (tmm)
REVERT: C   52 GLN cc_start: 0.7947 (mp10) cc_final: 0.7508 (mp10)
REVERT: C  235 ASP cc_start: 0.6932 (p0) cc_final: 0.6088 (t70)
REVERT: D   11 ASN cc_start: 0.8152 (t0) cc_final: 0.7855 (t0)
REVERT: D  235 ASP cc_start: 0.7528 (p0) cc_final: 0.6606 (t70)
REVERT: E   11 ASN cc_start: 0.8091 (t0) cc_final: 0.7835 (t0)
REVERT: E   19 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.6974 (mm)
REVERT: E  173 ASP cc_start: 0.7373 (m-30) cc_final: 0.6868 (m-30)
REVERT: E  189 ILE cc_start: 0.8635 (pt) cc_final: 0.8076 (pt)
REVERT: E  201 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7408 (mm-40)
  outliers start: 32
  outliers final: 24
  residues processed: 151
  average time/residue: 0.1596
  time to fit residues: 37.7910
Evaluate side-chains
  160 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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 B residue   50 LEU
Chi-restraints excluded: chain B residue   52 GLN
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   73 TYR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  199 GLU
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   96 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue   96 THR
Chi-restraints excluded: chain D residue  170 ASP
Chi-restraints excluded: chain D residue  190 ASN
Chi-restraints excluded: chain D residue  254 THR
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   53 TRP
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  201 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0770
   chunk 38 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.3342

-------------------------------------------------------------------------------
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**
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** 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 = 0.4965 r_free = 0.4965 target = 0.218123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.152711 restraints weight = 12099.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.158142 restraints weight = 8262.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.161437 restraints weight = 6600.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9475  Z= 0.137
  Angle     :  0.572   7.192  12865  Z= 0.299
  Chirality :  0.045   0.212   1395
  Planarity :  0.005   0.054   1665
  Dihedral  :  4.586  17.892   1280
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.71 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.25), residues: 1145
  helix:  0.72 (0.27), residues: 315
  sheet: -0.97 (0.27), residues: 380
  loop : -0.02 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  53 
 HIS   0.003   0.001   HIS A 175 
 PHE   0.015   0.002   PHE B 200 
 TYR   0.023   0.001   TYR E  55 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  388)
  hydrogen bonds       : angle       5.00355 ( 1125)
  covalent geometry    : bond        0.00325 ( 9475)
  covalent geometry    : angle       0.57169 (12865)

*********************** 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
  161 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7733 (mp10) cc_final: 0.7414 (mp10)
REVERT: A  201 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7171 (mm110)
REVERT: B   50 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7814 (mp)
REVERT: B   52 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7237 (mp10)
REVERT: B   73 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7141 (t80)
REVERT: B  130 GLN cc_start: 0.7959 (tp40) cc_final: 0.7568 (tm-30)
REVERT: B  189 ILE cc_start: 0.8793 (pt) cc_final: 0.8483 (pt)
REVERT: C   11 ASN cc_start: 0.8129 (t0) cc_final: 0.7879 (t0)
REVERT: C   19 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7168 (pt)
REVERT: C   31 MET cc_start: 0.7199 (mtt) cc_final: 0.6014 (tmm)
REVERT: C   52 GLN cc_start: 0.7925 (mp10) cc_final: 0.7481 (mp10)
REVERT: C  235 ASP cc_start: 0.7047 (p0) cc_final: 0.6074 (t70)
REVERT: D   11 ASN cc_start: 0.8180 (t0) cc_final: 0.7878 (t0)
REVERT: D  235 ASP cc_start: 0.7626 (p0) cc_final: 0.6651 (t0)
REVERT: E   11 ASN cc_start: 0.8097 (t0) cc_final: 0.7845 (t0)
REVERT: E   19 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.6829 (mm)
REVERT: E  173 ASP cc_start: 0.7378 (m-30) cc_final: 0.6870 (m-30)
REVERT: E  189 ILE cc_start: 0.8621 (pt) cc_final: 0.8068 (pt)
REVERT: E  201 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7252 (mm-40)
  outliers start: 33
  outliers final: 24
  residues processed: 148
  average time/residue: 0.1475
  time to fit residues: 33.8193
Evaluate side-chains
  158 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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 B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   73 TYR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain C residue   19 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   96 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue   96 THR
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   96 THR
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  201 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    0.0070
   chunk 37 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 109 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0870
   chunk 111 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** 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 = 0.5000 r_free = 0.5000 target = 0.221686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.156218 restraints weight = 12250.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.161840 restraints weight = 8204.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.165370 restraints weight = 6511.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.4398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9475  Z= 0.110
  Angle     :  0.543   7.018  12865  Z= 0.283
  Chirality :  0.044   0.218   1395
  Planarity :  0.005   0.054   1665
  Dihedral  :  4.325  16.849   1280
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.21 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.25), residues: 1145
  helix:  0.95 (0.27), residues: 315
  sheet: -0.92 (0.27), residues: 380
  loop :  0.19 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  53 
 HIS   0.003   0.001   HIS A 175 
 PHE   0.012   0.001   PHE C 200 
 TYR   0.023   0.001   TYR E  55 
 ARG   0.005   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  388)
  hydrogen bonds       : angle       4.78406 ( 1125)
  covalent geometry    : bond        0.00254 ( 9475)
  covalent geometry    : angle       0.54291 (12865)

********************** 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
  169 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7266 (pt)
REVERT: A   52 GLN cc_start: 0.7622 (mp10) cc_final: 0.7313 (mp10)
REVERT: A  201 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7077 (mm110)
REVERT: B   50 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7752 (mp)
REVERT: B   52 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7091 (mp10)
REVERT: B   73 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7095 (t80)
REVERT: B  189 ILE cc_start: 0.8781 (pt) cc_final: 0.8455 (pt)
REVERT: B  200 PHE cc_start: 0.7460 (p90) cc_final: 0.6918 (p90)
REVERT: C   11 ASN cc_start: 0.8061 (t0) cc_final: 0.7819 (t0)
REVERT: C   19 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7188 (pt)
REVERT: C   31 MET cc_start: 0.7167 (mtt) cc_final: 0.6056 (tmm)
REVERT: C   52 GLN cc_start: 0.7751 (mp10) cc_final: 0.7322 (mp10)
REVERT: C  235 ASP cc_start: 0.7070 (p0) cc_final: 0.6092 (t70)
REVERT: D   11 ASN cc_start: 0.8116 (t0) cc_final: 0.7875 (t0)
REVERT: D  235 ASP cc_start: 0.7693 (p0) cc_final: 0.6743 (t0)
REVERT: E   11 ASN cc_start: 0.8037 (t0) cc_final: 0.7819 (t0)
REVERT: E   19 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.6865 (mm)
REVERT: E  173 ASP cc_start: 0.7347 (m-30) cc_final: 0.6851 (m-30)
REVERT: E  189 ILE cc_start: 0.8611 (pt) cc_final: 0.7966 (pt)
REVERT: E  198 TRP cc_start: 0.7023 (m100) cc_final: 0.6639 (m100)
REVERT: E  201 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7157 (mm-40)
  outliers start: 29
  outliers final: 20
  residues processed: 155
  average time/residue: 0.1634
  time to fit residues: 38.5473
Evaluate side-chains
  161 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
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 B residue   50 LEU
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   73 TYR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain C residue   19 ILE
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   96 THR
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   53 TRP
Chi-restraints excluded: chain D residue   92 CYS
Chi-restraints excluded: chain D residue   96 THR
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   53 TRP
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  102 ILE
Chi-restraints excluded: chain E residue  201 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 81 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.4986

-------------------------------------------------------------------------------
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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 190 ASN
** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 ASN ** 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 = 0.4920 r_free = 0.4920 target = 0.213848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.149152 restraints weight = 12487.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.154190 restraints weight = 8711.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.157347 restraints weight = 7054.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9475  Z= 0.211
  Angle     :  0.665  11.012  12865  Z= 0.348
  Chirality :  0.048   0.238   1395
  Planarity :  0.005   0.053   1665
  Dihedral  :  4.963  18.920   1280
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.61 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1145
  helix:  0.35 (0.26), residues: 320
  sheet: -1.01 (0.28), residues: 350
  loop : -0.27 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  53 
 HIS   0.004   0.001   HIS C 175 
 PHE   0.017   0.002   PHE C 200 
 TYR   0.031   0.002   TYR C  55 
 ARG   0.005   0.001   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04719 (  388)
  hydrogen bonds       : angle       5.42838 ( 1125)
  covalent geometry    : bond        0.00502 ( 9475)
  covalent geometry    : angle       0.66504 (12865)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4632.09 seconds
wall clock time: 83 minutes 1.15 seconds (4981.15 seconds total)