Starting phenix.real_space_refine
on Thu Jul 31 05:43:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xku_22225/07_2025/6xku_22225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xku_22225/07_2025/6xku_22225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xku_22225/07_2025/6xku_22225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xku_22225/07_2025/6xku_22225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xku_22225/07_2025/6xku_22225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xku_22225/07_2025/6xku_22225.cif"
  }
  resolution = 4.2
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe     10      7.16       5
     S      78      5.16       5
     C    8578      2.51       5
     N    2155      2.21       5
     O    2258      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13079
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "E"
      Number of atoms: 1365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1365
          Classifications: {'peptide': 181}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 170}
    Chain: "R"
      Number of atoms: 1365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1365
          Classifications: {'peptide': 181}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 170}
    Chain: "C"
      Number of atoms: 3244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3244
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393}
          Chain breaks: 1
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 233
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 90
    Chain: "D"
      Number of atoms: 1801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1801
          Classifications: {'peptide': 235}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 15, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 20
    Chain: "P"
      Number of atoms: 3244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3244
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393}
          Chain breaks: 1
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 233
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 90
    Chain: "Q"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1794
          Classifications: {'peptide': 235}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 15, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 23
    Chain: "E"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'FES': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'FES': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 86
          Unusual residues: {'HEC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEC': 1}
          Classifications: {'undetermined': 1}
    Chain: "P"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 86
          Unusual residues: {'HEC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "Q"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEC': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    933  SG  CYS E 133      30.892  60.280  26.108  0.25105.87           S
  ATOM   1079  SG  CYS E 153      31.686  57.930  23.427  0.25107.21           S
  ATOM   2298  SG  CYS R 133      82.864  27.948  41.694  0.25105.87           S
  ATOM   2444  SG  CYS R 153      83.981  31.374  41.102  0.25107.21           S

  Residues with excluded nonbonded symmetry interactions: 53
    residue:
      pdb=" N   MET E 129 " occ=0.25
      ... (6 atoms not shown)
      pdb=" CE  MET E 129 " occ=0.25
    residue:
      pdb=" N   GLY E 131 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY E 131 " occ=0.25
    residue:
      pdb=" N   VAL E 132 " occ=0.25
      ... (5 atoms not shown)
      pdb=" CG2 VAL E 132 " occ=0.25
    residue:
      pdb=" N   CYS E 133 " occ=0.25
      ... (4 atoms not shown)
      pdb=" SG  CYS E 133 " occ=0.25
    residue:
      pdb=" N   THR E 134 " occ=0.25
      ... (5 atoms not shown)
      pdb=" CG2 THR E 134 " occ=0.25
    residue:
      pdb=" N   HIS E 135 " occ=0.25
      ... (8 atoms not shown)
      pdb=" NE2 HIS E 135 " occ=0.25
    residue:
      pdb=" N   LEU E 136 " occ=0.25
      ... (6 atoms not shown)
      pdb=" CD2 LEU E 136 " occ=0.25
    residue:
      pdb=" N   GLY E 137 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY E 137 " occ=0.25
    residue:
      pdb=" N   CYS E 138 " occ=0.25
      ... (4 atoms not shown)
      pdb=" SG  CYS E 138 " occ=0.25
    residue:
      pdb=" N   VAL E 139 " occ=0.25
      ... (5 atoms not shown)
      pdb=" CG2 VAL E 139 " occ=0.25
    residue:
      pdb=" N   PRO E 140 " occ=0.25
      ... (5 atoms not shown)
      pdb=" CD  PRO E 140 " occ=0.25
    residue:
      pdb=" N   GLY E 142 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY E 142 " occ=0.25
    ... (remaining 41 not shown)
  Time building chain proxies: 8.09, per 1000 atoms: 0.62
  Number of scatterers: 13079
  At special positions: 0
  Unit cell: (114.24, 99.28, 110.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe     10     26.01
     S      78     16.00
     O    2258      8.00
     N    2155      7.00
     C    8578      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 138 " - pdb=" SG  CYS E 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 138 " - pdb=" SG  CYS R 155 " distance=2.03

  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=10, symmetry=0
  Number of additional bonds: simple=10, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.95
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FES E 501 "
        pdb="FE2  FES E 501 " - pdb=" ND1 HIS E 135 "
        pdb="FE2  FES E 501 " - pdb=" ND1 HIS E 156 "
        pdb="FE1  FES E 501 " - pdb=" SG  CYS E 153 "
        pdb="FE1  FES E 501 " - pdb=" SG  CYS E 133 "
      pdb=" FES R 501 "
        pdb="FE2  FES R 501 " - pdb=" ND1 HIS R 156 "
        pdb="FE2  FES R 501 " - pdb=" ND1 HIS R 135 "
        pdb="FE1  FES R 501 " - pdb=" SG  CYS R 133 "
        pdb="FE1  FES R 501 " - pdb=" SG  CYS R 153 "
      Number of angles added : 6


  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3056

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      51.6% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'E' and resid 11 through 35
      Proline residue:  E  33  - end of helix
    Processing helix  chain 'E' and resid 41 through 49
      removed outlier: 3.857A  pdb=" N   ALA E  46 " --> pdb=" O   ALA E  42 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   MET E  47 " --> pdb=" O   ASP E  43 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA E  48 " --> pdb=" O   VAL E  44 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER E  49 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 87
    Processing helix  chain 'E' and resid 109 through 114
    Processing helix  chain 'R' and resid 12 through 37
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 41 through 46
      removed outlier: 3.562A  pdb=" N   ALA R  46 " --> pdb=" O   ALA R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 87
    Processing helix  chain 'R' and resid 109 through 114
    Processing helix  chain 'C' and resid 14 through 19
    Processing helix  chain 'C' and resid 23 through 33
      removed outlier: 3.764A  pdb=" N   GLY C  27 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 66
    Processing helix  chain 'C' and resid 75 through 86
    Processing helix  chain 'C' and resid 90 through 118
      removed outlier: 3.757A  pdb=" N   SER C 102 " --> pdb=" O   ALA C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 148
      removed outlier: 3.860A  pdb=" N   TRP C 129 " --> pdb=" O   ARG C 125 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL C 148 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 169
      removed outlier: 3.624A  pdb=" N   TRP C 157 " --> pdb=" O   GLN C 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE C 166 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY C 167 " --> pdb=" O   THR C 163 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ILE C 169 " --> pdb=" O   LEU C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 182
      removed outlier: 3.668A  pdb=" N   ILE C 176 " --> pdb=" O   ILE C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 199
    Processing helix  chain 'C' and resid 200 through 219
      removed outlier: 3.961A  pdb=" N   VAL C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE C 216 " --> pdb=" O   HIS C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 270
    Processing helix  chain 'C' and resid 276 through 281
    Processing helix  chain 'C' and resid 298 through 308
      removed outlier: 4.406A  pdb=" N   PHE C 308 " --> pdb=" O   ILE C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 321
    Processing helix  chain 'C' and resid 327 through 346
      removed outlier: 3.849A  pdb=" N   MET C 343 " --> pdb=" O   ALA C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 349
      No H-bonds generated for 'chain 'C' and resid 347 through 349'
    Processing helix  chain 'C' and resid 356 through 359
    Processing helix  chain 'C' and resid 360 through 381
    Processing helix  chain 'C' and resid 388 through 415
      removed outlier: 5.576A  pdb=" N   LEU C 408 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
      Proline residue:  C 409  - end of helix
    Processing helix  chain 'D' and resid 19 through 33
      removed outlier: 3.629A  pdb=" N   LEU D  23 " --> pdb=" O   ASP D  19 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU D  32 " --> pdb=" O   GLN D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 37
    Processing helix  chain 'D' and resid 44 through 49
    Processing helix  chain 'D' and resid 57 through 67
    Processing helix  chain 'D' and resid 127 through 136
    Processing helix  chain 'D' and resid 201 through 218
    Processing helix  chain 'D' and resid 220 through 250
    Processing helix  chain 'P' and resid 14 through 19
    Processing helix  chain 'P' and resid 23 through 33
      removed outlier: 3.762A  pdb=" N   GLY P  27 " --> pdb=" O   LEU P  23 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ILE P  33 " --> pdb=" O   VAL P  29 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 46 through 66
    Processing helix  chain 'P' and resid 75 through 86
    Processing helix  chain 'P' and resid 90 through 118
      removed outlier: 3.754A  pdb=" N   SER P 102 " --> pdb=" O   ALA P  98 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 125 through 148
      removed outlier: 3.860A  pdb=" N   TRP P 129 " --> pdb=" O   ARG P 125 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL P 148 " --> pdb=" O   PHE P 144 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 153 through 169
      removed outlier: 3.623A  pdb=" N   TRP P 157 " --> pdb=" O   GLN P 153 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE P 166 " --> pdb=" O   ILE P 162 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY P 167 " --> pdb=" O   THR P 163 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE P 169 " --> pdb=" O   LEU P 165 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 172 through 182
      removed outlier: 3.668A  pdb=" N   ILE P 176 " --> pdb=" O   ILE P 172 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 187 through 199
    Processing helix  chain 'P' and resid 200 through 219
      removed outlier: 3.957A  pdb=" N   VAL P 204 " --> pdb=" O   LEU P 200 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE P 216 " --> pdb=" O   HIS P 212 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 246 through 270
    Processing helix  chain 'P' and resid 276 through 281
    Processing helix  chain 'P' and resid 298 through 308
      removed outlier: 4.406A  pdb=" N   PHE P 308 " --> pdb=" O   ILE P 304 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 316 through 321
    Processing helix  chain 'P' and resid 327 through 346
      removed outlier: 3.848A  pdb=" N   MET P 343 " --> pdb=" O   ALA P 339 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 347 through 349
      No H-bonds generated for 'chain 'P' and resid 347 through 349'
    Processing helix  chain 'P' and resid 356 through 359
    Processing helix  chain 'P' and resid 360 through 381
    Processing helix  chain 'P' and resid 388 through 415
      removed outlier: 5.576A  pdb=" N   LEU P 408 " --> pdb=" O   PHE P 404 " (cutoff:3.500A)
      Proline residue:  P 409  - end of helix
    Processing helix  chain 'Q' and resid 19 through 33
      removed outlier: 3.627A  pdb=" N   LEU Q  23 " --> pdb=" O   ASP Q  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU Q  32 " --> pdb=" O   GLN Q  28 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 34 through 37
    Processing helix  chain 'Q' and resid 44 through 49
      removed outlier: 3.567A  pdb=" N   THR Q  47 " --> pdb=" O   PRO Q  44 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU Q  48 " --> pdb=" O   ILE Q  45 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA Q  49 " --> pdb=" O   ARG Q  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 44 through 49'
    Processing helix  chain 'Q' and resid 57 through 67
    Processing helix  chain 'Q' and resid 127 through 136
    Processing helix  chain 'Q' and resid 201 through 218
    Processing helix  chain 'Q' and resid 220 through 250
    Processing sheet with id=AA1, first strand: chain 'E' and resid 50 through 51
      removed outlier: 3.606A  pdb=" N   ALA E 181 " --> pdb=" O   LYS E 189 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 67
    Processing sheet with id=AA3, first strand: chain 'E' and resid 141 through 145
      removed outlier: 4.682A  pdb=" N   ASP E 143 " --> pdb=" O   GLY E 150 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   GLY E 150 " --> pdb=" O   ASP E 143 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TRP E 151 " --> pdb=" O   TYR E 160 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER E 158 " --> pdb=" O   CYS E 153 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'R' and resid 50 through 52
      removed outlier: 3.607A  pdb=" N   ALA R 181 " --> pdb=" O   LYS R 189 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'R' and resid 64 through 67
    Processing sheet with id=AA6, first strand: chain 'R' and resid 141 through 145
      removed outlier: 4.684A  pdb=" N   ASP R 143 " --> pdb=" O   GLY R 150 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   GLY R 150 " --> pdb=" O   ASP R 143 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   TRP R 151 " --> pdb=" O   TYR R 160 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER R 158 " --> pdb=" O   CYS R 153 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 153 through 155
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 153 through 155

    626 hydrogen bonds defined for protein.
    1806 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.00

  Time building geometry restraints manager: 4.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.41: 5785
        1.41 -     1.61: 7562
        1.61 -     1.80: 103
        1.80 -     2.00: 31
        2.00 -     2.20: 28
  Bond restraints: 13509
  Sorted by residual:
  bond pdb=" CAC HEC C 501 "
       pdb=" CBC HEC C 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.324  0.220 2.00e-02 2.50e+03 1.21e+02
  bond pdb=" CAC HEC P 501 "
       pdb=" CBC HEC P 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.324  0.220 2.00e-02 2.50e+03 1.20e+02
  bond pdb=" CAB HEC P 501 "
       pdb=" CBB HEC P 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.336  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C2D HEC C 501 "
       pdb=" C3D HEC C 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.336  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" CAB HEC C 501 "
       pdb=" CBB HEC C 501 "
    ideal  model  delta    sigma   weight residual
    1.544  1.337  0.207 2.00e-02 2.50e+03 1.08e+02
  ... (remaining 13504 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 18209
        3.17 -     6.33: 264
        6.33 -     9.50: 27
        9.50 -    12.67: 4
       12.67 -    15.84: 16
  Bond angle restraints: 18520
  Sorted by residual:
  angle pdb="FE1  FES R 501 "
        pdb=" S2  FES R 501 "
        pdb="FE2  FES R 501 "
      ideal   model   delta    sigma   weight residual
      75.66   89.12  -13.46 1.14e+00 7.69e-01 1.39e+02
  angle pdb="FE1  FES E 501 "
        pdb=" S2  FES E 501 "
        pdb="FE2  FES E 501 "
      ideal   model   delta    sigma   weight residual
      75.66   89.08  -13.42 1.14e+00 7.69e-01 1.39e+02
  angle pdb=" S1  FES R 501 "
        pdb="FE2  FES R 501 "
        pdb=" S2  FES R 501 "
      ideal   model   delta    sigma   weight residual
     104.33   90.93   13.40 1.14e+00 7.69e-01 1.38e+02
  angle pdb=" S1  FES E 501 "
        pdb="FE2  FES E 501 "
        pdb=" S2  FES E 501 "
      ideal   model   delta    sigma   weight residual
     104.33   90.94   13.39 1.14e+00 7.69e-01 1.38e+02
  angle pdb=" S1  FES R 501 "
        pdb="FE1  FES R 501 "
        pdb=" S2  FES R 501 "
      ideal   model   delta    sigma   weight residual
     104.33   90.78   13.55 1.20e+00 6.94e-01 1.28e+02
  ... (remaining 18515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 6978
       17.90 -    35.81: 534
       35.81 -    53.71: 82
       53.71 -    71.61: 10
       71.61 -    89.52: 22
  Dihedral angle restraints: 7626
    sinusoidal: 2836
      harmonic: 4790
  Sorted by residual:
  dihedral pdb=" C2B HEC P 501 "
           pdb=" C3B HEC P 501 "
           pdb=" CAB HEC P 501 "
           pdb=" CBB HEC P 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  -22.34   82.34     2      1.00e+01 1.00e-02 4.71e+01
  dihedral pdb=" C2B HEC C 501 "
           pdb=" C3B HEC C 501 "
           pdb=" CAB HEC C 501 "
           pdb=" CBB HEC C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  -22.17   82.17     2      1.00e+01 1.00e-02 4.71e+01
  dihedral pdb=" C2C HEC P 502 "
           pdb=" C3C HEC P 502 "
           pdb=" CAC HEC P 502 "
           pdb=" CBC HEC P 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  -17.13   77.13     2      1.00e+01 1.00e-02 4.56e+01
  ... (remaining 7623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.146: 1917
       0.146 -    0.292: 40
       0.292 -    0.438: 1
       0.438 -    0.584: 10
       0.584 -    0.729: 2
  Chirality restraints: 1970
  Sorted by residual:
  chirality pdb=" CG  LEU Q 244 "
            pdb=" CB  LEU Q 244 "
            pdb=" CD1 LEU Q 244 "
            pdb=" CD2 LEU Q 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.86   -0.73 2.00e-01 2.50e+01 1.33e+01
  chirality pdb=" CG  LEU D 244 "
            pdb=" CB  LEU D 244 "
            pdb=" CD1 LEU D 244 "
            pdb=" CD2 LEU D 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.86   -0.73 2.00e-01 2.50e+01 1.33e+01
  chirality pdb=" CB  THR Q 198 "
            pdb=" CA  THR Q 198 "
            pdb=" OG1 THR Q 198 "
            pdb=" CG2 THR Q 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.03    0.52 2.00e-01 2.50e+01 6.86e+00
  ... (remaining 1967 not shown)

  Planarity restraints: 2327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC Q 501 "    0.010 2.00e-02 2.50e+03   4.12e-02 3.82e+01
        pdb=" C2C HEC Q 501 "   -0.109 2.00e-02 2.50e+03
        pdb=" C3C HEC Q 501 "    0.042 2.00e-02 2.50e+03
        pdb=" C4C HEC Q 501 "    0.007 2.00e-02 2.50e+03
        pdb=" CAC HEC Q 501 "    0.007 2.00e-02 2.50e+03
        pdb=" CHC HEC Q 501 "    0.018 2.00e-02 2.50e+03
        pdb=" CHD HEC Q 501 "   -0.007 2.00e-02 2.50e+03
        pdb=" CMC HEC Q 501 "    0.031 2.00e-02 2.50e+03
        pdb=" NC  HEC Q 501 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC D 501 "   -0.010 2.00e-02 2.50e+03   4.11e-02 3.81e+01
        pdb=" C2C HEC D 501 "    0.109 2.00e-02 2.50e+03
        pdb=" C3C HEC D 501 "   -0.042 2.00e-02 2.50e+03
        pdb=" C4C HEC D 501 "   -0.007 2.00e-02 2.50e+03
        pdb=" CAC HEC D 501 "   -0.007 2.00e-02 2.50e+03
        pdb=" CHC HEC D 501 "   -0.018 2.00e-02 2.50e+03
        pdb=" CHD HEC D 501 "    0.007 2.00e-02 2.50e+03
        pdb=" CMC HEC D 501 "   -0.031 2.00e-02 2.50e+03
        pdb=" NC  HEC D 501 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 222 "   -0.021 2.00e-02 2.50e+03   4.29e-02 1.84e+01
        pdb=" C   ASN C 222 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ASN C 222 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ASN C 223 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 2324 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 167
        2.57 -     3.15: 11801
        3.15 -     3.73: 19465
        3.73 -     4.32: 27251
        4.32 -     4.90: 45455
  Nonbonded interactions: 104139
  Sorted by model distance:
  nonbonded pdb=" O   THR E 186 "
            pdb=" OG1 THR E 187 "
     model   vdw
     1.987 3.040
  nonbonded pdb=" O   THR R 186 "
            pdb=" OG1 THR R 187 "
     model   vdw
     1.987 3.040
  nonbonded pdb=" OG  SER P 120 "
            pdb=" ND2 ASN P 222 "
     model   vdw
     1.988 3.120
  nonbonded pdb=" NH2 ARG P 306 "
            pdb=" O   MET P 383 "
     model   vdw
     2.007 3.120
  nonbonded pdb=" NH2 ARG C 306 "
            pdb=" O   MET C 383 "
     model   vdw
     2.007 3.120
  ... (remaining 104134 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'P'
}
ncs_group {
  reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 84 through 257 or resid 501))
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=0.98
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:             0.850
  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:             0.020
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.890
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
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      :  0.010   0.220  13529  Z= 0.468
  Angle     :  1.028  23.204  18530  Z= 0.622
  Chirality :  0.069   0.729   1970
  Planarity :  0.006   0.082   2327
  Dihedral  : 13.797  89.516   4564
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 25.66
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 16.47 %
    Favored  : 83.17 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.80 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -4.29 (0.17), residues: 1658
  helix: -1.64 (0.16), residues: 782
  sheet: -3.48 (0.49), residues: 64
  loop : -4.18 (0.18), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 296 
 HIS   0.010   0.001   HIS P 111 
 PHE   0.021   0.001   PHE C 104 
 TYR   0.010   0.001   TYR C 297 
 ARG   0.002   0.000   ARG R  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14710 (  626)
  hydrogen bonds       : angle       6.99370 ( 1806)
  metal coordination   : bond        0.01210 (    8)
  metal coordination   : angle      14.21024 (    6)
  SS BOND              : bond        0.00111 (    2)
  SS BOND              : angle       0.57340 (    4)
  covalent geometry    : bond        0.00939 (13509)
  covalent geometry    : angle       0.99581 (18520)
  Misc. bond           : bond        0.14972 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  555 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 553
  time to evaluate  : 1.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   13 ASP cc_start: 0.3644 (p0) cc_final: 0.3358 (t0)
REVERT: E   37 GLN cc_start: 0.8527 (pp30) cc_final: 0.8304 (pp30)
REVERT: E  102 ASN cc_start: 0.7091 (p0) cc_final: 0.6481 (p0)
REVERT: E  167 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7610 (mtp85)
REVERT: E  174 ASN cc_start: 0.5896 (p0) cc_final: 0.5194 (p0)
REVERT: R   76 ARG cc_start: 0.6091 (tpt170) cc_final: 0.5598 (tpt-90)
REVERT: C   39 LYS cc_start: 0.6276 (mttt) cc_final: 0.5490 (pttt)
REVERT: C   70 THR cc_start: 0.8989 (m) cc_final: 0.8387 (p)
REVERT: C   94 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7875 (ttt-90)
REVERT: C  110 ILE cc_start: 0.9314 (mt) cc_final: 0.8858 (mm)
REVERT: C  139 MET cc_start: 0.8107 (ptm) cc_final: 0.7763 (ptp)
REVERT: C  175 SER cc_start: 0.8596 (m) cc_final: 0.8347 (t)
REVERT: C  296 TRP cc_start: 0.8221 (p-90) cc_final: 0.7885 (p-90)
REVERT: C  299 LEU cc_start: 0.8509 (mt) cc_final: 0.8252 (mt)
REVERT: C  302 TYR cc_start: 0.8342 (t80) cc_final: 0.8140 (t80)
REVERT: C  374 PHE cc_start: 0.8692 (t80) cc_final: 0.8443 (t80)
REVERT: D  210 SER cc_start: 0.9550 (m) cc_final: 0.9220 (t)
REVERT: D  254 LYS cc_start: 0.6759 (mttm) cc_final: 0.6222 (tptt)
REVERT: P  175 SER cc_start: 0.8368 (m) cc_final: 0.7896 (t)
REVERT: Q   32 GLU cc_start: 0.6689 (mt-10) cc_final: 0.5868 (mt-10)
REVERT: Q  103 MET cc_start: 0.8767 (tpp) cc_final: 0.8533 (mmm)
REVERT: Q  134 TYR cc_start: 0.7640 (t80) cc_final: 0.7132 (t80)
REVERT: Q  155 ASN cc_start: 0.5972 (t0) cc_final: 0.5419 (t0)
REVERT: Q  188 VAL cc_start: 0.7600 (t) cc_final: 0.7003 (m)
REVERT: Q  222 VAL cc_start: 0.7975 (m) cc_final: 0.7767 (p)
REVERT: Q  229 LEU cc_start: 0.8754 (tp) cc_final: 0.8537 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 555
  average time/residue: 0.2638
  time to fit residues: 204.7350
Evaluate side-chains
  268 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 267
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 140 optimal weight:    0.9990
   chunk 125 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 150 optimal weight:    8.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 100 ASN
C  72 HIS
C 192 ASN
C 217 HIS
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 291 HIS
** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  72 HIS
P 222 ASN
P 282 GLN
Q 177 HIS
** Q 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 204 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.113837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.092364 restraints weight = 38276.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.094458 restraints weight = 21058.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.095667 restraints weight = 14487.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.304  13529  Z= 0.171
  Angle     :  0.788  14.481  18530  Z= 0.374
  Chirality :  0.046   0.188   1970
  Planarity :  0.006   0.077   2327
  Dihedral  :  8.821  89.007   1858
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 11.88 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.80 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.19), residues: 1658
  helix: -0.05 (0.17), residues: 827
  sheet: -2.11 (0.65), residues: 52
  loop : -3.41 (0.20), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 126 
 HIS   0.005   0.001   HIS P 217 
 PHE   0.020   0.002   PHE P 401 
 TYR   0.021   0.002   TYR P 199 
 ARG   0.006   0.001   ARG R 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05071 (  626)
  hydrogen bonds       : angle       4.94454 ( 1806)
  metal coordination   : bond        0.01376 (    8)
  metal coordination   : angle       8.67183 (    6)
  SS BOND              : bond        0.00042 (    2)
  SS BOND              : angle       0.64770 (    4)
  covalent geometry    : bond        0.00396 (13509)
  covalent geometry    : angle       0.77289 (18520)
  Misc. bond           : bond        0.16814 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 393
  time to evaluate  : 2.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   70 LYS cc_start: 0.8218 (pttp) cc_final: 0.7925 (pttp)
REVERT: E   93 LEU cc_start: 0.6761 (mm) cc_final: 0.6533 (mm)
REVERT: E  107 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: R   35 ILE cc_start: 0.9354 (mm) cc_final: 0.9128 (mm)
REVERT: R   50 ILE cc_start: 0.7246 (tp) cc_final: 0.6969 (tp)
REVERT: R  127 LEU cc_start: 0.7456 (mp) cc_final: 0.7243 (mp)
REVERT: R  130 LEU cc_start: 0.8999 (mt) cc_final: 0.8223 (mt)
REVERT: R  143 ASP cc_start: 0.7363 (m-30) cc_final: 0.6967 (m-30)
REVERT: C   39 LYS cc_start: 0.7576 (mttt) cc_final: 0.5827 (pttp)
REVERT: C   70 THR cc_start: 0.9207 (m) cc_final: 0.8759 (p)
REVERT: C   93 MET cc_start: 0.9385 (mmm) cc_final: 0.8791 (mmm)
REVERT: C  110 ILE cc_start: 0.9568 (mt) cc_final: 0.9246 (tt)
REVERT: C  175 SER cc_start: 0.9060 (m) cc_final: 0.8696 (t)
REVERT: C  296 TRP cc_start: 0.8607 (p-90) cc_final: 0.8037 (p-90)
REVERT: C  306 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8212 (ttt-90)
REVERT: D  180 TRP cc_start: 0.7581 (m100) cc_final: 0.6788 (m100)
REVERT: D  195 GLU cc_start: 0.7719 (mp0) cc_final: 0.7506 (mp0)
REVERT: P  120 SER cc_start: 0.8910 (m) cc_final: 0.8698 (m)
REVERT: P  121 TYR cc_start: 0.7585 (p90) cc_final: 0.6676 (p90)
REVERT: P  305 LEU cc_start: 0.8887 (mt) cc_final: 0.8664 (mt)
REVERT: P  343 MET cc_start: 0.8328 (mtp) cc_final: 0.8103 (ttm)
REVERT: P  374 PHE cc_start: 0.9090 (t80) cc_final: 0.8766 (t80)
REVERT: P  378 THR cc_start: 0.9530 (m) cc_final: 0.9291 (p)
REVERT: P  390 ASP cc_start: 0.8291 (p0) cc_final: 0.8063 (p0)
REVERT: Q   28 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7812 (tp-100)
REVERT: Q   43 VAL cc_start: 0.9257 (t) cc_final: 0.8913 (p)
REVERT: Q   96 MET cc_start: 0.8590 (mmp) cc_final: 0.7881 (mmm)
REVERT: Q  204 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8343 (tp-100)
REVERT: Q  214 MET cc_start: 0.8551 (tpp) cc_final: 0.7952 (tpt)
REVERT: Q  222 VAL cc_start: 0.8721 (m) cc_final: 0.8503 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 395
  average time/residue: 0.2817
  time to fit residues: 161.0318
Evaluate side-chains
  245 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 243
  time to evaluate  : 1.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 146 optimal weight:    0.0050
   chunk 143 optimal weight:    3.9990
   chunk 136 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0170
   chunk 92 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0010
   chunk 66 optimal weight:    3.9990
   chunk 127 optimal weight:    0.5980
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 ASN
** C  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 ASN
C 217 HIS
** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 282 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.102872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.083141 restraints weight = 40552.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.085353 restraints weight = 21847.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.086741 restraints weight = 14512.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.306  13529  Z= 0.149
  Angle     :  0.733  12.862  18530  Z= 0.349
  Chirality :  0.045   0.175   1970
  Planarity :  0.006   0.058   2327
  Dihedral  :  8.691  89.780   1858
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 11.70 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.72 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.62 (0.20), residues: 1658
  helix:  0.56 (0.18), residues: 815
  sheet: -0.97 (0.73), residues: 52
  loop : -3.02 (0.20), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 151 
 HIS   0.005   0.001   HIS C  68 
 PHE   0.026   0.001   PHE C 330 
 TYR   0.034   0.001   TYR C 109 
 ARG   0.006   0.001   ARG C  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04596 (  626)
  hydrogen bonds       : angle       4.73152 ( 1806)
  metal coordination   : bond        0.00890 (    8)
  metal coordination   : angle       8.56415 (    6)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.37909 (    4)
  covalent geometry    : bond        0.00315 (13509)
  covalent geometry    : angle       0.71665 (18520)
  Misc. bond           : bond        0.15953 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 365
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   93 LEU cc_start: 0.6818 (mm) cc_final: 0.6597 (mm)
REVERT: E  145 SER cc_start: 0.8632 (m) cc_final: 0.8343 (m)
REVERT: R   66 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8898 (tmtt)
REVERT: R  130 LEU cc_start: 0.9210 (mt) cc_final: 0.8524 (mt)
REVERT: C   39 LYS cc_start: 0.7768 (mttt) cc_final: 0.5943 (pttp)
REVERT: C   70 THR cc_start: 0.9220 (m) cc_final: 0.8763 (p)
REVERT: C   93 MET cc_start: 0.9452 (mmm) cc_final: 0.8777 (mmm)
REVERT: C   94 ARG cc_start: 0.8602 (ttt-90) cc_final: 0.8256 (ttt-90)
REVERT: C  110 ILE cc_start: 0.9509 (mt) cc_final: 0.9262 (tt)
REVERT: C  133 MET cc_start: 0.8596 (mmp) cc_final: 0.8358 (mmm)
REVERT: C  175 SER cc_start: 0.8677 (m) cc_final: 0.8376 (t)
REVERT: C  296 TRP cc_start: 0.8782 (p-90) cc_final: 0.8197 (p-90)
REVERT: C  372 LEU cc_start: 0.9261 (tp) cc_final: 0.8862 (tt)
REVERT: D   22 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8344 (tp-100)
REVERT: D   27 PHE cc_start: 0.8871 (t80) cc_final: 0.8556 (t80)
REVERT: D   31 ASN cc_start: 0.9191 (p0) cc_final: 0.8755 (p0)
REVERT: D   81 ASP cc_start: 0.7745 (t0) cc_final: 0.7536 (t0)
REVERT: D  134 TYR cc_start: 0.9035 (t80) cc_final: 0.8787 (t80)
REVERT: D  180 TRP cc_start: 0.7573 (m100) cc_final: 0.6952 (m100)
REVERT: D  232 MET cc_start: 0.8002 (tmm) cc_final: 0.7765 (tmm)
REVERT: P  120 SER cc_start: 0.9068 (m) cc_final: 0.8790 (m)
REVERT: P  121 TYR cc_start: 0.7845 (p90) cc_final: 0.7113 (p90)
REVERT: P  295 GLU cc_start: 0.8478 (tp30) cc_final: 0.8274 (tp30)
REVERT: P  334 ILE cc_start: 0.8953 (tp) cc_final: 0.8724 (tp)
REVERT: P  350 ASP cc_start: 0.7241 (m-30) cc_final: 0.6448 (m-30)
REVERT: P  374 PHE cc_start: 0.9068 (t80) cc_final: 0.8834 (t80)
REVERT: P  378 THR cc_start: 0.9540 (m) cc_final: 0.9241 (p)
REVERT: Q   28 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7142 (tp-100)
REVERT: Q   32 GLU cc_start: 0.7880 (mt-10) cc_final: 0.6982 (mt-10)
REVERT: Q   41 LYS cc_start: 0.7839 (pttp) cc_final: 0.7594 (pttp)
REVERT: Q   47 THR cc_start: 0.8108 (p) cc_final: 0.7710 (p)
REVERT: Q   76 SER cc_start: 0.7949 (p) cc_final: 0.7699 (p)
REVERT: Q   78 GLU cc_start: 0.6743 (mp0) cc_final: 0.6110 (mp0)
REVERT: Q   96 MET cc_start: 0.8548 (mmp) cc_final: 0.7832 (mmm)
REVERT: Q  100 LEU cc_start: 0.9199 (mt) cc_final: 0.8902 (mt)
REVERT: Q  155 ASN cc_start: 0.6399 (t0) cc_final: 0.5649 (t0)
REVERT: Q  158 PHE cc_start: 0.8691 (t80) cc_final: 0.8379 (t80)
REVERT: Q  204 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8474 (tp-100)
REVERT: Q  214 MET cc_start: 0.8596 (tpp) cc_final: 0.7726 (tpt)
REVERT: Q  222 VAL cc_start: 0.8731 (m) cc_final: 0.8460 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 366
  average time/residue: 0.2400
  time to fit residues: 129.6173
Evaluate side-chains
  256 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 125 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 111 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 HIS
C  99 ASN
C 217 HIS
D 159 GLN
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.100786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.080697 restraints weight = 39680.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.082887 restraints weight = 21151.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.084301 restraints weight = 14043.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.203  13529  Z= 0.143
  Angle     :  0.706  11.627  18530  Z= 0.335
  Chirality :  0.045   0.171   1970
  Planarity :  0.005   0.060   2327
  Dihedral  :  8.514  87.367   1858
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.80 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  3.36 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.23 (0.21), residues: 1658
  helix:  0.75 (0.18), residues: 827
  sheet: -0.45 (0.69), residues: 58
  loop : -2.74 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 151 
 HIS   0.005   0.001   HIS P  82 
 PHE   0.022   0.001   PHE C 374 
 TYR   0.041   0.002   TYR P 199 
 ARG   0.007   0.001   ARG C 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04402 (  626)
  hydrogen bonds       : angle       4.59062 ( 1806)
  metal coordination   : bond        0.00857 (    8)
  metal coordination   : angle       9.29191 (    6)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       0.31703 (    4)
  covalent geometry    : bond        0.00344 (13509)
  covalent geometry    : angle       0.68609 (18520)
  Misc. bond           : bond        0.11419 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 351
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  145 SER cc_start: 0.8651 (m) cc_final: 0.8384 (m)
REVERT: R   50 ILE cc_start: 0.7810 (tp) cc_final: 0.7573 (tp)
REVERT: R   66 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8716 (tmtt)
REVERT: R  130 LEU cc_start: 0.9274 (mt) cc_final: 0.8866 (mt)
REVERT: C   39 LYS cc_start: 0.7896 (mttt) cc_final: 0.5931 (tttm)
REVERT: C   70 THR cc_start: 0.9200 (m) cc_final: 0.8767 (p)
REVERT: C   84 MET cc_start: 0.8943 (mmm) cc_final: 0.8137 (mmm)
REVERT: C   93 MET cc_start: 0.9480 (mmm) cc_final: 0.8835 (mmm)
REVERT: C   94 ARG cc_start: 0.8697 (ttt-90) cc_final: 0.7436 (ttt180)
REVERT: C  110 ILE cc_start: 0.9600 (mt) cc_final: 0.9249 (tt)
REVERT: C  139 MET cc_start: 0.8395 (ptp) cc_final: 0.8147 (ptt)
REVERT: C  175 SER cc_start: 0.8740 (m) cc_final: 0.8431 (t)
REVERT: C  199 TYR cc_start: 0.9216 (t80) cc_final: 0.8888 (t80)
REVERT: C  296 TRP cc_start: 0.8829 (p-90) cc_final: 0.8322 (p-90)
REVERT: D   22 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8188 (tp-100)
REVERT: D   27 PHE cc_start: 0.9039 (t80) cc_final: 0.8793 (t80)
REVERT: D   31 ASN cc_start: 0.9202 (p0) cc_final: 0.8780 (p0)
REVERT: D   68 LEU cc_start: 0.9076 (mt) cc_final: 0.8844 (mt)
REVERT: D   87 MET cc_start: 0.8277 (mtm) cc_final: 0.8031 (mtm)
REVERT: D  103 MET cc_start: 0.8871 (tpp) cc_final: 0.8547 (tpp)
REVERT: D  232 MET cc_start: 0.8186 (tmm) cc_final: 0.7897 (tmm)
REVERT: P  121 TYR cc_start: 0.8044 (p90) cc_final: 0.7479 (p90)
REVERT: P  165 LEU cc_start: 0.9235 (mp) cc_final: 0.8944 (mp)
REVERT: P  252 ASP cc_start: 0.8653 (p0) cc_final: 0.8424 (p0)
REVERT: P  260 LEU cc_start: 0.9757 (mp) cc_final: 0.9493 (mm)
REVERT: P  270 MET cc_start: 0.8122 (mpp) cc_final: 0.7894 (mpp)
REVERT: P  287 SER cc_start: 0.8810 (m) cc_final: 0.8401 (p)
REVERT: P  295 GLU cc_start: 0.8492 (tp30) cc_final: 0.8234 (tp30)
REVERT: P  305 LEU cc_start: 0.8947 (mt) cc_final: 0.8731 (mt)
REVERT: P  350 ASP cc_start: 0.7582 (m-30) cc_final: 0.6774 (m-30)
REVERT: P  374 PHE cc_start: 0.9136 (t80) cc_final: 0.8905 (t80)
REVERT: P  378 THR cc_start: 0.9490 (m) cc_final: 0.9165 (p)
REVERT: Q   28 GLN cc_start: 0.8463 (tp-100) cc_final: 0.7909 (tp-100)
REVERT: Q   41 LYS cc_start: 0.8021 (pttp) cc_final: 0.7655 (pttp)
REVERT: Q   43 VAL cc_start: 0.9228 (t) cc_final: 0.8912 (p)
REVERT: Q   78 GLU cc_start: 0.6827 (mp0) cc_final: 0.6344 (mp0)
REVERT: Q   96 MET cc_start: 0.8313 (mmp) cc_final: 0.7698 (mmm)
REVERT: Q  132 TYR cc_start: 0.8315 (t80) cc_final: 0.7971 (t80)
REVERT: Q  155 ASN cc_start: 0.6775 (t0) cc_final: 0.5971 (t0)
REVERT: Q  204 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8572 (tp-100)
  outliers start: 3
  outliers final: 2
  residues processed: 352
  average time/residue: 0.2571
  time to fit residues: 133.3358
Evaluate side-chains
  256 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0030
   chunk 54 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0040
   chunk 136 optimal weight:    0.8980
   chunk 143 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0670
   chunk 141 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.5942

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 159 HIS
C  99 ASN
C 192 ASN
C 217 HIS
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.101615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.082041 restraints weight = 40967.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.084106 restraints weight = 22708.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.085318 restraints weight = 15501.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.170  13529  Z= 0.133
  Angle     :  0.694  12.188  18530  Z= 0.327
  Chirality :  0.044   0.169   1970
  Planarity :  0.005   0.058   2327
  Dihedral  :  8.336  86.343   1858
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.62 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.56 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.96 (0.21), residues: 1658
  helix:  0.93 (0.18), residues: 827
  sheet: -0.39 (0.70), residues: 58
  loop : -2.54 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 151 
 HIS   0.004   0.001   HIS C 291 
 PHE   0.010   0.001   PHE D 138 
 TYR   0.031   0.001   TYR C 109 
 ARG   0.006   0.001   ARG R  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  626)
  hydrogen bonds       : angle       4.45981 ( 1806)
  metal coordination   : bond        0.00672 (    8)
  metal coordination   : angle       9.84183 (    6)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.20967 (    4)
  covalent geometry    : bond        0.00319 (13509)
  covalent geometry    : angle       0.67157 (18520)
  Misc. bond           : bond        0.10643 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 347
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   47 MET cc_start: 0.7920 (tpt) cc_final: 0.7401 (tpp)
REVERT: E  145 SER cc_start: 0.8637 (m) cc_final: 0.8398 (m)
REVERT: R   66 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8754 (tmtt)
REVERT: R   70 LYS cc_start: 0.9107 (mptt) cc_final: 0.8853 (mppt)
REVERT: R   90 LEU cc_start: 0.8381 (mp) cc_final: 0.8085 (tt)
REVERT: R  130 LEU cc_start: 0.9235 (mt) cc_final: 0.8803 (mt)
REVERT: C   39 LYS cc_start: 0.7790 (mttt) cc_final: 0.5891 (tttm)
REVERT: C   70 THR cc_start: 0.9182 (m) cc_final: 0.8777 (p)
REVERT: C   93 MET cc_start: 0.9322 (mmm) cc_final: 0.8405 (mmm)
REVERT: C  175 SER cc_start: 0.8790 (m) cc_final: 0.8458 (t)
REVERT: C  296 TRP cc_start: 0.8701 (p-90) cc_final: 0.8351 (p-90)
REVERT: D   22 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8231 (tp-100)
REVERT: D   87 MET cc_start: 0.8217 (mtm) cc_final: 0.7988 (mtm)
REVERT: D  241 MET cc_start: 0.9138 (ttm) cc_final: 0.8891 (ttt)
REVERT: P   79 SER cc_start: 0.9440 (p) cc_final: 0.9211 (m)
REVERT: P  187 ASP cc_start: 0.9087 (t0) cc_final: 0.8397 (m-30)
REVERT: P  188 ASN cc_start: 0.9037 (p0) cc_final: 0.8441 (p0)
REVERT: P  252 ASP cc_start: 0.8538 (p0) cc_final: 0.8237 (p0)
REVERT: P  305 LEU cc_start: 0.8773 (mt) cc_final: 0.8463 (mt)
REVERT: P  365 MET cc_start: 0.8290 (tmm) cc_final: 0.8008 (tmm)
REVERT: P  378 THR cc_start: 0.9498 (m) cc_final: 0.9259 (p)
REVERT: Q   28 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7714 (tp-100)
REVERT: Q   41 LYS cc_start: 0.8197 (pttp) cc_final: 0.7897 (pttp)
REVERT: Q   78 GLU cc_start: 0.6951 (mp0) cc_final: 0.6730 (mp0)
REVERT: Q  132 TYR cc_start: 0.8269 (t80) cc_final: 0.7882 (t80)
REVERT: Q  155 ASN cc_start: 0.6737 (t0) cc_final: 0.6338 (t0)
REVERT: Q  156 LYS cc_start: 0.7850 (tptp) cc_final: 0.7588 (tptt)
REVERT: Q  204 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8490 (tp-100)
REVERT: Q  235 LEU cc_start: 0.9380 (mp) cc_final: 0.9137 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 348
  average time/residue: 0.2284
  time to fit residues: 117.9578
Evaluate side-chains
  242 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 124 optimal weight:    5.9990
   chunk 155 optimal weight:    7.9990
   chunk 119 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 156 optimal weight:    0.8980
   chunk 142 optimal weight:    5.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 HIS
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 GLN
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 276 HIS
P 291 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.092248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.072324 restraints weight = 41298.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.074298 restraints weight = 22490.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.075542 restraints weight = 15081.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.6082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.227  13529  Z= 0.254
  Angle     :  0.832  14.385  18530  Z= 0.393
  Chirality :  0.048   0.201   1970
  Planarity :  0.006   0.060   2327
  Dihedral  :  8.555  89.995   1858
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 12.12 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.14 (0.21), residues: 1658
  helix:  0.74 (0.18), residues: 823
  sheet: -0.60 (0.68), residues: 60
  loop : -2.56 (0.22), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP P 400 
 HIS   0.008   0.002   HIS E 156 
 PHE   0.032   0.002   PHE P 105 
 TYR   0.022   0.002   TYR C 199 
 ARG   0.008   0.001   ARG C  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05051 (  626)
  hydrogen bonds       : angle       4.81405 ( 1806)
  metal coordination   : bond        0.01793 (    8)
  metal coordination   : angle       8.64893 (    6)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.27362 (    4)
  covalent geometry    : bond        0.00628 (13509)
  covalent geometry    : angle       0.81749 (18520)
  Misc. bond           : bond        0.11166 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLN cc_start: 0.8021 (tt0) cc_final: 0.7780 (pp30)
REVERT: E  128 VAL cc_start: 0.8531 (m) cc_final: 0.8274 (m)
REVERT: E  145 SER cc_start: 0.8684 (m) cc_final: 0.8452 (m)
REVERT: E  182 PHE cc_start: 0.7186 (m-10) cc_final: 0.6683 (m-80)
REVERT: R   66 LYS cc_start: 0.9261 (tmtt) cc_final: 0.8978 (tptp)
REVERT: R  129 MET cc_start: 0.9022 (ttm) cc_final: 0.8757 (ttt)
REVERT: R  130 LEU cc_start: 0.9325 (mt) cc_final: 0.8742 (mt)
REVERT: R  175 LEU cc_start: 0.9558 (mt) cc_final: 0.9284 (mt)
REVERT: C   39 LYS cc_start: 0.8021 (mttt) cc_final: 0.6011 (ttpt)
REVERT: C   84 MET cc_start: 0.9341 (mmm) cc_final: 0.8981 (mmm)
REVERT: C   93 MET cc_start: 0.9552 (mmm) cc_final: 0.9132 (mmm)
REVERT: C  139 MET cc_start: 0.8389 (ptp) cc_final: 0.8155 (ptt)
REVERT: C  175 SER cc_start: 0.8838 (m) cc_final: 0.8591 (t)
REVERT: C  252 ASP cc_start: 0.8611 (m-30) cc_final: 0.8407 (m-30)
REVERT: C  296 TRP cc_start: 0.8915 (p-90) cc_final: 0.8669 (p-90)
REVERT: D   22 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8255 (tp-100)
REVERT: D   68 LEU cc_start: 0.9331 (mt) cc_final: 0.9077 (mt)
REVERT: D  103 MET cc_start: 0.8755 (tpp) cc_final: 0.8545 (tpp)
REVERT: D  180 TRP cc_start: 0.8290 (m100) cc_final: 0.7475 (m100)
REVERT: D  232 MET cc_start: 0.8405 (tmm) cc_final: 0.8125 (tmm)
REVERT: P   58 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8788 (tp40)
REVERT: P  118 TYR cc_start: 0.8786 (m-80) cc_final: 0.8431 (m-10)
REVERT: P  133 MET cc_start: 0.9049 (mmm) cc_final: 0.8638 (mmm)
REVERT: P  147 TYR cc_start: 0.8352 (t80) cc_final: 0.8063 (t80)
REVERT: Q   28 GLN cc_start: 0.8528 (tp-100) cc_final: 0.7885 (tp40)
REVERT: Q   46 ARG cc_start: 0.9171 (pmt-80) cc_final: 0.8234 (ptt-90)
REVERT: Q   78 GLU cc_start: 0.6880 (mp0) cc_final: 0.6460 (mp0)
REVERT: Q   87 MET cc_start: 0.7854 (mmt) cc_final: 0.7482 (mmt)
REVERT: Q  155 ASN cc_start: 0.7325 (t0) cc_final: 0.6894 (t0)
REVERT: Q  204 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8324 (tp-100)
REVERT: Q  218 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8743 (tt0)
REVERT: Q  235 LEU cc_start: 0.9432 (mp) cc_final: 0.9203 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 307
  average time/residue: 0.2355
  time to fit residues: 108.3003
Evaluate side-chains
  221 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 155 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 120 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0970
   chunk 137 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 ASN
C 192 ASN
C 217 HIS
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 246 ASN
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 291 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.095881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.076280 restraints weight = 39959.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.078358 restraints weight = 21573.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.079373 restraints weight = 14266.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.6291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.152  13529  Z= 0.143
  Angle     :  0.717  10.483  18530  Z= 0.347
  Chirality :  0.046   0.209   1970
  Planarity :  0.005   0.058   2327
  Dihedral  :  8.298  86.244   1858
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.19 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.60 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.89 (0.21), residues: 1658
  helix:  1.00 (0.18), residues: 825
  sheet: -0.11 (0.73), residues: 55
  loop : -2.53 (0.22), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  47 
 HIS   0.021   0.001   HIS P 291 
 PHE   0.015   0.001   PHE P 104 
 TYR   0.036   0.002   TYR P 199 
 ARG   0.005   0.001   ARG R  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04482 (  626)
  hydrogen bonds       : angle       4.42385 ( 1806)
  metal coordination   : bond        0.00499 (    8)
  metal coordination   : angle       8.72572 (    6)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.23835 (    4)
  covalent geometry    : bond        0.00350 (13509)
  covalent geometry    : angle       0.69967 (18520)
  Misc. bond           : bond        0.08055 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 325
  time to evaluate  : 1.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   78 ASP cc_start: 0.6431 (p0) cc_final: 0.5871 (m-30)
REVERT: E  145 SER cc_start: 0.8672 (m) cc_final: 0.8447 (m)
REVERT: E  161 ASP cc_start: 0.7633 (p0) cc_final: 0.7125 (p0)
REVERT: E  182 PHE cc_start: 0.6954 (m-10) cc_final: 0.6486 (m-80)
REVERT: R  129 MET cc_start: 0.9013 (ttm) cc_final: 0.8721 (ttt)
REVERT: R  130 LEU cc_start: 0.9261 (mt) cc_final: 0.8626 (mt)
REVERT: C   39 LYS cc_start: 0.7950 (mttt) cc_final: 0.6092 (tttm)
REVERT: C   84 MET cc_start: 0.9338 (mmm) cc_final: 0.9004 (mmm)
REVERT: C   93 MET cc_start: 0.9466 (mmm) cc_final: 0.8922 (mmm)
REVERT: C  175 SER cc_start: 0.8829 (m) cc_final: 0.8596 (t)
REVERT: C  228 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7115 (tm-30)
REVERT: C  296 TRP cc_start: 0.8821 (p-90) cc_final: 0.8610 (p-90)
REVERT: D   22 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8345 (tp-100)
REVERT: D   68 LEU cc_start: 0.9312 (mt) cc_final: 0.9063 (mt)
REVERT: D   87 MET cc_start: 0.8380 (mtm) cc_final: 0.8165 (mtm)
REVERT: D  214 MET cc_start: 0.8882 (tpp) cc_final: 0.8665 (tpp)
REVERT: P   58 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8480 (tp-100)
REVERT: P   67 MET cc_start: 0.9136 (mmm) cc_final: 0.8919 (mmm)
REVERT: P  118 TYR cc_start: 0.8709 (m-80) cc_final: 0.8238 (m-10)
REVERT: P  133 MET cc_start: 0.8995 (mmm) cc_final: 0.8735 (mmm)
REVERT: P  295 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: Q   28 GLN cc_start: 0.8502 (tp-100) cc_final: 0.7845 (tp40)
REVERT: Q  155 ASN cc_start: 0.7036 (t0) cc_final: 0.6686 (t0)
REVERT: Q  204 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8278 (tp-100)
REVERT: Q  235 LEU cc_start: 0.9443 (mp) cc_final: 0.9231 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 327
  average time/residue: 0.2964
  time to fit residues: 146.8689
Evaluate side-chains
  233 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 2.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 96 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 107 optimal weight:    0.1980
   chunk 121 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 HIS
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 GLN
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.096147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.076544 restraints weight = 39880.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.078669 restraints weight = 21516.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.079847 restraints weight = 14180.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.6518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.136  13529  Z= 0.143
  Angle     :  0.726  10.601  18530  Z= 0.349
  Chirality :  0.046   0.195   1970
  Planarity :  0.005   0.057   2327
  Dihedral  :  8.228  86.087   1858
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.62 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.87 (0.21), residues: 1658
  helix:  1.02 (0.18), residues: 825
  sheet: -0.11 (0.72), residues: 55
  loop : -2.53 (0.22), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP E 151 
 HIS   0.005   0.001   HIS P 276 
 PHE   0.022   0.001   PHE P 104 
 TYR   0.028   0.001   TYR P 199 
 ARG   0.007   0.000   ARG Q 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04411 (  626)
  hydrogen bonds       : angle       4.37963 ( 1806)
  metal coordination   : bond        0.00408 (    8)
  metal coordination   : angle       7.99140 (    6)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       0.12597 (    4)
  covalent geometry    : bond        0.00356 (13509)
  covalent geometry    : angle       0.71153 (18520)
  Misc. bond           : bond        0.06870 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 1.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  145 SER cc_start: 0.8781 (m) cc_final: 0.8531 (t)
REVERT: E  182 PHE cc_start: 0.6885 (m-10) cc_final: 0.6418 (m-80)
REVERT: R   35 ILE cc_start: 0.9566 (mm) cc_final: 0.9284 (tp)
REVERT: R  107 GLU cc_start: 0.8579 (tp30) cc_final: 0.8374 (tp30)
REVERT: R  129 MET cc_start: 0.8982 (ttm) cc_final: 0.8702 (ttt)
REVERT: R  130 LEU cc_start: 0.9249 (mt) cc_final: 0.8658 (mt)
REVERT: C   39 LYS cc_start: 0.7959 (mttt) cc_final: 0.6028 (tttm)
REVERT: C   46 ILE cc_start: 0.8773 (pt) cc_final: 0.8378 (tp)
REVERT: C   84 MET cc_start: 0.9351 (mmm) cc_final: 0.9114 (mmm)
REVERT: C   93 MET cc_start: 0.9454 (mmm) cc_final: 0.8839 (mmm)
REVERT: C  154 MET cc_start: 0.7858 (tpp) cc_final: 0.7494 (tpp)
REVERT: C  175 SER cc_start: 0.8839 (m) cc_final: 0.8593 (t)
REVERT: C  228 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7064 (tm-30)
REVERT: C  293 VAL cc_start: 0.7612 (t) cc_final: 0.7315 (p)
REVERT: C  349 LEU cc_start: 0.8842 (mt) cc_final: 0.8617 (mt)
REVERT: D   22 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8370 (tp-100)
REVERT: D   28 GLN cc_start: 0.8447 (tm130) cc_final: 0.8125 (tm-30)
REVERT: D   68 LEU cc_start: 0.9314 (mt) cc_final: 0.9054 (mt)
REVERT: D  180 TRP cc_start: 0.8320 (m100) cc_final: 0.7604 (m100)
REVERT: D  214 MET cc_start: 0.9019 (tpp) cc_final: 0.8332 (tpt)
REVERT: D  229 LEU cc_start: 0.9108 (mm) cc_final: 0.8093 (mm)
REVERT: P   58 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8607 (tp-100)
REVERT: P  165 LEU cc_start: 0.9067 (mp) cc_final: 0.8858 (mp)
REVERT: Q   28 GLN cc_start: 0.8570 (tp-100) cc_final: 0.7899 (tp-100)
REVERT: Q   46 ARG cc_start: 0.9078 (pmt-80) cc_final: 0.8322 (ptt-90)
REVERT: Q   78 GLU cc_start: 0.6854 (mp0) cc_final: 0.6464 (mp0)
REVERT: Q   87 MET cc_start: 0.7560 (mmt) cc_final: 0.7329 (mmt)
REVERT: Q   94 ASP cc_start: 0.7114 (m-30) cc_final: 0.6909 (m-30)
REVERT: Q  101 SER cc_start: 0.8995 (m) cc_final: 0.8616 (p)
REVERT: Q  155 ASN cc_start: 0.7163 (t0) cc_final: 0.6816 (t0)
REVERT: Q  204 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8196 (tp-100)
REVERT: Q  218 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8224 (tt0)
REVERT: Q  221 LEU cc_start: 0.9238 (mp) cc_final: 0.8916 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 316
  average time/residue: 0.3160
  time to fit residues: 150.5349
Evaluate side-chains
  237 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 2.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 32 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 120 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 127 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
E  62 GLN
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 177 GLN
C 217 HIS
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 291 HIS
D  28 GLN
D 246 ASN
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.096293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.076930 restraints weight = 40149.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.078890 restraints weight = 21854.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.080217 restraints weight = 14652.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.6677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.149  13529  Z= 0.143
  Angle     :  0.736  10.096  18530  Z= 0.355
  Chirality :  0.046   0.208   1970
  Planarity :  0.005   0.055   2327
  Dihedral  :  8.258  87.302   1858
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.80 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.04 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.81 (0.21), residues: 1658
  helix:  1.07 (0.18), residues: 825
  sheet:  0.25 (0.78), residues: 47
  loop : -2.50 (0.22), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP E 151 
 HIS   0.007   0.001   HIS C 291 
 PHE   0.018   0.001   PHE P 104 
 TYR   0.018   0.002   TYR C 136 
 ARG   0.007   0.001   ARG Q 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04346 (  626)
  hydrogen bonds       : angle       4.38423 ( 1806)
  metal coordination   : bond        0.00458 (    8)
  metal coordination   : angle       7.74504 (    6)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.10734 (    4)
  covalent geometry    : bond        0.00351 (13509)
  covalent geometry    : angle       0.72273 (18520)
  Misc. bond           : bond        0.07236 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 311
  time to evaluate  : 1.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  128 VAL cc_start: 0.8580 (m) cc_final: 0.8311 (m)
REVERT: E  145 SER cc_start: 0.8814 (m) cc_final: 0.8554 (t)
REVERT: E  182 PHE cc_start: 0.6838 (m-10) cc_final: 0.6386 (m-80)
REVERT: R   35 ILE cc_start: 0.9562 (mm) cc_final: 0.9280 (tp)
REVERT: R   70 LYS cc_start: 0.9240 (mptt) cc_final: 0.8865 (mppt)
REVERT: R  129 MET cc_start: 0.8999 (ttm) cc_final: 0.8685 (ttt)
REVERT: C   39 LYS cc_start: 0.7964 (mttt) cc_final: 0.6018 (tttm)
REVERT: C   46 ILE cc_start: 0.8670 (pt) cc_final: 0.8340 (tp)
REVERT: C   84 MET cc_start: 0.9324 (mmm) cc_final: 0.9043 (mmm)
REVERT: C   93 MET cc_start: 0.9425 (mmm) cc_final: 0.8789 (mmm)
REVERT: C  175 SER cc_start: 0.8848 (m) cc_final: 0.8608 (t)
REVERT: C  349 LEU cc_start: 0.8809 (mt) cc_final: 0.8598 (mt)
REVERT: D   22 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8352 (tp-100)
REVERT: D   28 GLN cc_start: 0.8473 (tm130) cc_final: 0.8167 (tm-30)
REVERT: D   31 ASN cc_start: 0.9207 (p0) cc_final: 0.8816 (p0)
REVERT: D   68 LEU cc_start: 0.9330 (mt) cc_final: 0.9080 (mt)
REVERT: D   87 MET cc_start: 0.8273 (mtm) cc_final: 0.7952 (mtm)
REVERT: D  180 TRP cc_start: 0.8128 (m100) cc_final: 0.7363 (m100)
REVERT: D  214 MET cc_start: 0.8976 (tpp) cc_final: 0.8303 (tpt)
REVERT: D  229 LEU cc_start: 0.8685 (mm) cc_final: 0.8309 (mm)
REVERT: D  232 MET cc_start: 0.8279 (ppp) cc_final: 0.8077 (ppp)
REVERT: P   58 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8587 (tp-100)
REVERT: P  118 TYR cc_start: 0.8917 (m-80) cc_final: 0.8036 (m-10)
REVERT: Q   28 GLN cc_start: 0.8575 (tp-100) cc_final: 0.7902 (tp-100)
REVERT: Q   46 ARG cc_start: 0.9060 (pmt-80) cc_final: 0.8268 (ptt-90)
REVERT: Q   78 GLU cc_start: 0.6876 (mp0) cc_final: 0.6508 (mp0)
REVERT: Q   87 MET cc_start: 0.7584 (mmt) cc_final: 0.7339 (mmt)
REVERT: Q  101 SER cc_start: 0.8851 (m) cc_final: 0.8498 (p)
REVERT: Q  155 ASN cc_start: 0.7268 (t0) cc_final: 0.6844 (t0)
REVERT: Q  180 TRP cc_start: 0.8435 (m-90) cc_final: 0.8051 (m-90)
REVERT: Q  204 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8190 (tp-100)
REVERT: Q  241 MET cc_start: 0.8396 (ttp) cc_final: 0.8169 (tmm)
REVERT: Q  245 THR cc_start: 0.9114 (p) cc_final: 0.8781 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 312
  average time/residue: 0.2287
  time to fit residues: 107.5155
Evaluate side-chains
  239 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 152 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0040
   chunk 82 optimal weight:    0.2980
   chunk 29 optimal weight:   10.0000
   chunk 105 optimal weight:    0.8980
   chunk 149 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 15 optimal weight:    0.2980
   overall best weight:    0.2490

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 ASN
C 217 HIS
C 222 ASN
C 291 HIS
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.098416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.078899 restraints weight = 39842.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.081109 restraints weight = 21335.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.082536 restraints weight = 14002.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.6858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.127  13529  Z= 0.131
  Angle     :  0.725  10.083  18530  Z= 0.350
  Chirality :  0.045   0.206   1970
  Planarity :  0.005   0.055   2327
  Dihedral  :  8.128  86.734   1858
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.49 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.64 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.75 (0.21), residues: 1658
  helix:  1.15 (0.18), residues: 825
  sheet:  0.13 (0.79), residues: 47
  loop : -2.49 (0.22), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP E 151 
 HIS   0.007   0.001   HIS C 217 
 PHE   0.019   0.001   PHE E  73 
 TYR   0.034   0.001   TYR P 136 
 ARG   0.008   0.000   ARG Q 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  626)
  hydrogen bonds       : angle       4.31645 ( 1806)
  metal coordination   : bond        0.00393 (    8)
  metal coordination   : angle       7.82511 (    6)
  SS BOND              : bond        0.00047 (    2)
  SS BOND              : angle       0.12991 (    4)
  covalent geometry    : bond        0.00298 (13509)
  covalent geometry    : angle       0.71169 (18520)
  Misc. bond           : bond        0.07275 (   10)

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

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

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3316 Ramachandran restraints generated.
    1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 326
  time to evaluate  : 1.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  128 VAL cc_start: 0.8468 (m) cc_final: 0.8177 (m)
REVERT: E  145 SER cc_start: 0.8838 (m) cc_final: 0.8610 (t)
REVERT: E  182 PHE cc_start: 0.6734 (m-10) cc_final: 0.6305 (m-80)
REVERT: R   35 ILE cc_start: 0.9539 (mm) cc_final: 0.9254 (tp)
REVERT: R  129 MET cc_start: 0.9026 (ttm) cc_final: 0.8711 (ttt)
REVERT: C   39 LYS cc_start: 0.7858 (mttt) cc_final: 0.5966 (tttm)
REVERT: C   46 ILE cc_start: 0.8577 (pt) cc_final: 0.8291 (tp)
REVERT: C   93 MET cc_start: 0.9421 (mmm) cc_final: 0.8759 (mmm)
REVERT: C  133 MET cc_start: 0.8386 (mmp) cc_final: 0.8127 (mmm)
REVERT: C  175 SER cc_start: 0.8843 (m) cc_final: 0.8595 (t)
REVERT: C  222 ASN cc_start: 0.8604 (t160) cc_final: 0.8355 (t0)
REVERT: D   22 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8318 (tp-100)
REVERT: D   28 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8145 (tm-30)
REVERT: D   68 LEU cc_start: 0.9317 (mt) cc_final: 0.9079 (mt)
REVERT: D  101 SER cc_start: 0.9415 (m) cc_final: 0.9179 (p)
REVERT: D  103 MET cc_start: 0.8683 (tpp) cc_final: 0.8400 (tpp)
REVERT: D  134 TYR cc_start: 0.8919 (t80) cc_final: 0.8700 (t80)
REVERT: D  180 TRP cc_start: 0.8045 (m100) cc_final: 0.7397 (m100)
REVERT: D  214 MET cc_start: 0.8983 (tpp) cc_final: 0.8323 (tpt)
REVERT: D  229 LEU cc_start: 0.8795 (mm) cc_final: 0.8222 (mm)
REVERT: D  232 MET cc_start: 0.8341 (ppp) cc_final: 0.8139 (ppp)
REVERT: P  187 ASP cc_start: 0.8926 (t0) cc_final: 0.8191 (m-30)
REVERT: P  287 SER cc_start: 0.9010 (m) cc_final: 0.8621 (p)
REVERT: Q   28 GLN cc_start: 0.8571 (tp-100) cc_final: 0.7884 (tp-100)
REVERT: Q   46 ARG cc_start: 0.9059 (pmt-80) cc_final: 0.8252 (ptt-90)
REVERT: Q   78 GLU cc_start: 0.6963 (mp0) cc_final: 0.6508 (mp0)
REVERT: Q   87 MET cc_start: 0.7343 (mmt) cc_final: 0.7105 (mmt)
REVERT: Q  101 SER cc_start: 0.8845 (m) cc_final: 0.8298 (p)
REVERT: Q  155 ASN cc_start: 0.7113 (t0) cc_final: 0.6673 (t0)
REVERT: Q  180 TRP cc_start: 0.8419 (m-90) cc_final: 0.8201 (m-90)
REVERT: Q  204 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8218 (tp-100)
REVERT: Q  245 THR cc_start: 0.9113 (p) cc_final: 0.8787 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 326
  average time/residue: 0.2243
  time to fit residues: 109.8275
Evaluate side-chains
  244 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 143 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0970
   chunk 138 optimal weight:    6.9990
   chunk 136 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 88 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 156 optimal weight:    0.9990
   chunk 115 optimal weight:    0.0570
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
E  36 ASN
E  62 GLN
** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 HIS
D 246 ASN
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.079277 restraints weight = 39864.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.081415 restraints weight = 21409.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.082827 restraints weight = 14088.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.7043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.168  13529  Z= 0.132
  Angle     :  0.721   9.589  18530  Z= 0.347
  Chirality :  0.045   0.201   1970
  Planarity :  0.005   0.054   2327
  Dihedral  :  8.058  85.433   1858
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.19 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.72 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.74 (0.21), residues: 1658
  helix:  1.17 (0.18), residues: 825
  sheet: -0.22 (0.72), residues: 53
  loop : -2.50 (0.22), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP E 151 
 HIS   0.006   0.001   HIS C 217 
 PHE   0.024   0.001   PHE P 104 
 TYR   0.025   0.001   TYR C 136 
 ARG   0.008   0.000   ARG Q 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  626)
  hydrogen bonds       : angle       4.32477 ( 1806)
  metal coordination   : bond        0.00398 (    8)
  metal coordination   : angle       7.46266 (    6)
  SS BOND              : bond        0.00020 (    2)
  SS BOND              : angle       0.11780 (    4)
  covalent geometry    : bond        0.00310 (13509)
  covalent geometry    : angle       0.70897 (18520)
  Misc. bond           : bond        0.07865 (   10)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5245.42 seconds
wall clock time: 96 minutes 45.28 seconds (5805.28 seconds total)