Starting phenix.real_space_refine
on Fri Jul  3 10:45:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lai_62929/07_2026/9lai_62929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lai_62929/07_2026/9lai_62929.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lai_62929/07_2026/9lai_62929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lai_62929/07_2026/9lai_62929.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lai_62929/07_2026/9lai_62929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lai_62929/07_2026/9lai_62929.map"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P      20      5.49       5
     S      20      5.16       5
     Cl      5      4.86       5
     C    8890      2.51       5
     N    2034      2.21       5
     O    2431      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13400
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2529
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
    Chain: "B"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2529
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
    Chain: "C"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2529
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
    Chain: "E"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2529
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
    Chain: "D"
      Number of atoms: 2540
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 312, 2529
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
      Conformer: "B"
        Number of residues, atoms: 312, 2529
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2585
    Chain: "A"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 146
          Ad-hoc single atom residues: {' CL': 1}
          Unusual residues: {'PEE': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 176
          Ad-hoc single atom residues: {' CL': 1}
          Unusual residues: {'PEE': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 4}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 130
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 112
          Ad-hoc single atom residues: {' CL': 1}
          Unusual residues: {'PEE': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 2}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 192
          Ad-hoc single atom residues: {' CL': 1}
          Unusual residues: {'PEE': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Ad-hoc single atom residues: {' CL': 1}
          Unusual residues: {'PEE': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 1}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 44
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG D 293 " occ=0.51
      ... (20 atoms not shown)
      pdb=" NH2BARG D 293 " occ=0.49
  Time building chain proxies: 3.00, per 1000 atoms: 0.22
  Number of scatterers: 13400
  At special positions: 0
  Unit cell: (101.84, 95, 128.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      5     17.00
     S      20     16.00
     P      20     15.00
     O    2431      8.00
     N    2034      7.00
     C    8890      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 571.7 milliseconds
  

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3052

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 17 sheets defined
      38.2% alpha, 30.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 196 through 213
      removed outlier: 4.849A  pdb=" N   LEU A 203 " --> pdb=" O   PRO A 199 " (cutoff:3.500A)
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 214 through 218
      removed outlier: 3.636A  pdb=" N   SER A 218 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 244
      removed outlier: 3.955A  pdb=" N   THR A 244 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 282
    Processing helix  chain 'A' and resid 284 through 315
      removed outlier: 3.628A  pdb=" N   ALA A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ILE A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      Proline residue:  A 300  - end of helix
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 4.266A  pdb=" N   ILE B  71 " --> pdb=" O   PRO B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 196 through 214
      removed outlier: 5.046A  pdb=" N   LEU B 203 " --> pdb=" O   PRO B 199 " (cutoff:3.500A)
      Proline residue:  B 204  - end of helix
    Processing helix  chain 'B' and resid 215 through 218
      removed outlier: 3.683A  pdb=" N   SER B 218 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 215 through 218'
    Processing helix  chain 'B' and resid 220 through 244
      removed outlier: 4.114A  pdb=" N   THR B 244 " --> pdb=" O   ILE B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 282
    Processing helix  chain 'B' and resid 284 through 315
      removed outlier: 3.832A  pdb=" N   ARG B 296 " --> pdb=" O   THR B 292 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      Proline residue:  B 300  - end of helix
    Processing helix  chain 'C' and resid 57 through 61
      removed outlier: 4.001A  pdb=" N   VAL C  61 " --> pdb=" O   ARG C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
      removed outlier: 4.169A  pdb=" N   ILE C  71 " --> pdb=" O   PRO C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 196 through 214
      removed outlier: 5.028A  pdb=" N   LEU C 203 " --> pdb=" O   PRO C 199 " (cutoff:3.500A)
      Proline residue:  C 204  - end of helix
    Processing helix  chain 'C' and resid 215 through 218
      removed outlier: 3.749A  pdb=" N   SER C 218 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 215 through 218'
    Processing helix  chain 'C' and resid 220 through 244
      removed outlier: 4.005A  pdb=" N   THR C 244 " --> pdb=" O   ILE C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 282
    Processing helix  chain 'C' and resid 284 through 315
      removed outlier: 3.774A  pdb=" N   ARG C 296 " --> pdb=" O   THR C 292 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ILE C 297 " --> pdb=" O   ARG C 293 " (cutoff:3.500A)
      Proline residue:  C 300  - end of helix
    Processing helix  chain 'E' and resid 55 through 60
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 146 through 149
      removed outlier: 3.796A  pdb=" N   VAL E 149 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 146 through 149'
    Processing helix  chain 'E' and resid 196 through 201
      removed outlier: 3.532A  pdb=" N   ASN E 200 " --> pdb=" O   SER E 196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 214
      removed outlier: 3.709A  pdb=" N   MET E 205 " --> pdb=" O   ILE E 201 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E 206 " --> pdb=" O   ILE E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 215 through 218
      removed outlier: 3.704A  pdb=" N   SER E 218 " --> pdb=" O   ALA E 215 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 215 through 218'
    Processing helix  chain 'E' and resid 220 through 243
    Processing helix  chain 'E' and resid 253 through 282
    Processing helix  chain 'E' and resid 284 through 316
      removed outlier: 3.565A  pdb=" N   ALA E 288 " --> pdb=" O   GLN E 284 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE E 297 " --> pdb=" O   ARG E 293 " (cutoff:3.500A)
      Proline residue:  E 300  - end of helix
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 196 through 213
      removed outlier: 5.379A  pdb=" N   LEU D 203 " --> pdb=" O   PRO D 199 " (cutoff:3.500A)
      Proline residue:  D 204  - end of helix
    Processing helix  chain 'D' and resid 214 through 218
      removed outlier: 3.664A  pdb=" N   SER D 218 " --> pdb=" O   ALA D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 244
    Processing helix  chain 'D' and resid 253 through 282
    Processing helix  chain 'D' and resid 284 through 315
      removed outlier: 3.576A  pdb=" N   ALA D 288 " --> pdb=" O   GLN D 284 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE D 297 " --> pdb=" O  AARG D 293 " (cutoff:3.500A)
      Proline residue:  D 300  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 111
      removed outlier: 5.841A  pdb=" N   PHE A  42 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   LEU A  24 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   SER A  44 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   SER A  46 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   THR A  20 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 111
      removed outlier: 5.841A  pdb=" N   PHE A  42 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   LEU A  24 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   SER A  44 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   SER A  46 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   THR A  20 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   GLY A 150 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE A  22 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 65
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 3.514A  pdb=" N   LEU A 130 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ASP A 185 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ALA A 167 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   GLN A 187 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   PHE A 165 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ARG A 189 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 28
      removed outlier: 5.737A  pdb=" N   LEU B  24 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   PHE B  42 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B  43 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU B  45 " --> pdb=" O   TYR B 102 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR B 102 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLN B 101 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ILE B  92 " --> pdb=" O   GLN B 101 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU B 103 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL B  94 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 28
      removed outlier: 5.737A  pdb=" N   LEU B  24 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   PHE B  42 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LEU B  16 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ALA B 143 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   VAL B  18 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 5.540A  pdb=" N   VAL B 132 " --> pdb=" O   SER B 182 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER B 182 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER B 164 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   SER B 191 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   ILE B 162 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47
      removed outlier: 6.699A  pdb=" N   LEU C  16 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ALA C 143 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   VAL C  18 " --> pdb=" O   ALA C 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 64 through 65
      removed outlier: 4.833A  pdb=" N   VAL C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   ARG C 105 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   THR C  36 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   LEU C  30 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78
      removed outlier: 3.510A  pdb=" N   ILE C 190 " --> pdb=" O   GLN C 124 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   VAL C 132 " --> pdb=" O   SER C 182 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   SER C 182 " --> pdb=" O   VAL C 132 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   LYS C 183 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   VAL C 169 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ASP C 185 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ALA C 167 " --> pdb=" O   ASP C 185 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   GLN C 187 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   PHE C 165 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ARG C 189 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 65
      removed outlier: 5.839A  pdb=" N   VAL E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ARG E 105 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASP E  91 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TRP E  47 " --> pdb=" O   VAL E 100 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E  45 " --> pdb=" O   TYR E 102 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   THR E  36 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   SER E  29 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LYS E  38 " --> pdb=" O   CYS E  27 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   CYS E  27 " --> pdb=" O   LYS E  38 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ASN E  40 " --> pdb=" O   ILE E  25 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   LEU E  16 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   ALA E 143 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL E  18 " --> pdb=" O   ALA E 143 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 64 through 65
      removed outlier: 5.839A  pdb=" N   VAL E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ARG E 105 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASP E  91 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TRP E  47 " --> pdb=" O   VAL E 100 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E  45 " --> pdb=" O   TYR E 102 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   THR E  36 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   SER E  29 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LYS E  38 " --> pdb=" O   CYS E  27 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   CYS E  27 " --> pdb=" O   LYS E  38 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ASN E  40 " --> pdb=" O   ILE E  25 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78
      removed outlier: 3.566A  pdb=" N   SER E 182 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   ASP E 185 " --> pdb=" O   VAL E 168 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER E 164 " --> pdb=" O   ARG E 189 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   SER E 191 " --> pdb=" O   ILE E 162 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   ILE E 162 " --> pdb=" O   SER E 191 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 77 through 78
      removed outlier: 3.566A  pdb=" N   SER E 182 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 16 through 17
      removed outlier: 6.164A  pdb=" N   LEU D  16 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 94
      removed outlier: 3.584A  pdb=" N   LEU D  43 " --> pdb=" O   GLU D 104 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   THR D  36 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   SER D  29 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   LYS D  38 " --> pdb=" O   CYS D  27 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   CYS D  27 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ASN D  40 " --> pdb=" O   ILE D  25 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR D  23 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 78
      removed outlier: 7.262A  pdb=" N   LYS D 183 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   VAL D 169 " --> pdb=" O   LYS D 183 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ASP D 185 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ALA D 167 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   GLN D 187 " --> pdb=" O   PHE D 165 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   PHE D 165 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ARG D 189 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)

    628 hydrogen bonds defined for protein.
    1804 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2124
        1.32 -     1.44: 3678
        1.44 -     1.56: 7835
        1.56 -     1.69: 40
        1.69 -     1.81: 35
  Bond restraints: 13712
  Sorted by residual:
  bond pdb=" CB  TRP E 213 "
       pdb=" CG  TRP E 213 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.48e+00
  bond pdb=" C13 PEE B 405 "
       pdb=" C14 PEE B 405 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 2.00e-02 2.50e+03 1.09e+00
  bond pdb=" C13 PEE C 405 "
       pdb=" C14 PEE C 405 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" C13 PEE A 404 "
       pdb=" C14 PEE A 404 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 2.00e-02 2.50e+03 1.06e+00
  bond pdb=" CA  PRO E   7 "
       pdb=" C   PRO E   7 "
    ideal  model  delta    sigma   weight residual
    1.514  1.509  0.005 5.50e-03 3.31e+04 9.57e-01
  ... (remaining 13707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 17999
        1.21 -     2.42: 448
        2.42 -     3.63: 101
        3.63 -     4.83: 21
        4.83 -     6.04: 9
  Bond angle restraints: 18578
  Sorted by residual:
  angle pdb=" N   ILE D  25 "
        pdb=" CA  ILE D  25 "
        pdb=" C   ILE D  25 "
      ideal   model   delta    sigma   weight residual
     111.67  108.75    2.92 9.50e-01 1.11e+00 9.46e+00
  angle pdb=" N   ASP A 153 "
        pdb=" CA  ASP A 153 "
        pdb=" C   ASP A 153 "
      ideal   model   delta    sigma   weight residual
     113.38  110.70    2.68 1.17e+00 7.31e-01 5.25e+00
  angle pdb=" N   ILE C 201 "
        pdb=" CA  ILE C 201 "
        pdb=" C   ILE C 201 "
      ideal   model   delta    sigma   weight residual
     109.34  113.34   -4.00 2.08e+00 2.31e-01 3.70e+00
  angle pdb=" N   ILE B 201 "
        pdb=" CA  ILE B 201 "
        pdb=" C   ILE B 201 "
      ideal   model   delta    sigma   weight residual
     109.34  113.34   -4.00 2.08e+00 2.31e-01 3.70e+00
  angle pdb=" N   GLU E 243 "
        pdb=" CA  GLU E 243 "
        pdb=" C   GLU E 243 "
      ideal   model   delta    sigma   weight residual
     112.34  114.82   -2.48 1.30e+00 5.92e-01 3.63e+00
  ... (remaining 18573 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 8050
       35.36 -    70.72: 201
       70.72 -   106.09: 22
      106.09 -   141.45: 17
      141.45 -   176.81: 11
  Dihedral angle restraints: 8301
    sinusoidal: 3617
      harmonic: 4684
  Sorted by residual:
  dihedral pdb=" O2  PEE E 407 "
           pdb=" C1  PEE E 407 "
           pdb=" C2  PEE E 407 "
           pdb=" O3P PEE E 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.04  123.23  176.81     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C3  PEE E 407 "
           pdb=" C1  PEE E 407 "
           pdb=" C2  PEE E 407 "
           pdb=" O3P PEE E 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73 -111.72  174.45     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C4  PEE B 406 "
           pdb=" O4P PEE B 406 "
           pdb=" P   PEE B 406 "
           pdb=" O3P PEE B 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.78  -27.65 -160.57     1      3.00e+01 1.11e-03 2.07e+01
  ... (remaining 8298 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1199
       0.027 -    0.054: 516
       0.054 -    0.080: 195
       0.080 -    0.107: 139
       0.107 -    0.134: 47
  Chirality restraints: 2096
  Sorted by residual:
  chirality pdb=" CA  ILE D  71 "
            pdb=" N   ILE D  71 "
            pdb=" C   ILE D  71 "
            pdb=" CB  ILE D  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE E  73 "
            pdb=" N   ILE E  73 "
            pdb=" C   ILE E  73 "
            pdb=" CB  ILE E  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  PHE C 299 "
            pdb=" N   PHE C 299 "
            pdb=" C   PHE C 299 "
            pdb=" CB  PHE C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 2093 not shown)

  Planarity restraints: 2268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  67 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO B  68 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B  68 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  68 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 249 "    0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO D 250 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 250 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 250 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 249 "   -0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 250 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 250 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 250 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 2265 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2369
        2.77 -     3.31: 12092
        3.31 -     3.84: 20444
        3.84 -     4.37: 24137
        4.37 -     4.90: 43504
  Nonbonded interactions: 102546
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 227 "
            pdb=" OG1 THR A 231 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   ILE C  76 "
            pdb=" NH1 ARG C  85 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" O   LEU C 227 "
            pdb=" OG1 THR C 231 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLU B 163 "
            pdb=" NH1 ARG B 189 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OH  TYR D 102 "
            pdb=" OE2 GLU D 104 "
     model   vdw
     2.338 3.040
  ... (remaining 102541 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ 
name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15  \ 
or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 
2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name  \ 
O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 o \ 
r name C15 or name C16 or name C17 or name C18 or name C19))))
  selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ 
name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15  \ 
or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 
2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name  \ 
O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 o \ 
r name C15 or name C16 or name C17 or name C18 or name C19))))
  selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or resid 403 or (re \ 
sid 404 and (name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 
8 or name C19))))
  selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ 
name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15  \ 
or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 
2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name  \ 
O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 o \ 
r name C15 or name C16 or name C17 or name C18 or name C19))))
  selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ 
name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ 
 or name C17 or name C18 or name C20 or name C21 or name C22 or name C23 or name \ 
 C24 or name C3 or name O1P or name O2 or name O2P or name O3 or name O3P or nam \ 
e O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 \ 
 or name C15 or name C16 or name C17 or name C18 or name C19))))
}

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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.260
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
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      :  0.003   0.038  13712  Z= 0.135
  Angle     :  0.516   6.043  18578  Z= 0.270
  Chirality :  0.042   0.134   2096
  Planarity :  0.004   0.042   2268
  Dihedral  : 17.811 176.809   5249
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  6.50 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.22), residues: 1553
  helix:  2.98 (0.21), residues: 518
  sheet: -1.07 (0.27), residues: 360
  loop : -1.34 (0.23), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  51 
 TYR   0.013   0.001   TYR D 254 
 PHE   0.011   0.001   PHE B 156 
 TRP   0.006   0.001   TRP A 160 
 HIS   0.002   0.001   HIS B 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 (13712)
  covalent geometry    : angle       0.51606 /  0.27 (18578)
  hydrogen bonds       : bond        0.17014 / 11.00 (  579)
  hydrogen bonds       : angle       6.64171 /  4.71 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 194
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  280 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8420 (ttpp)
REVERT: C   88 ASP cc_start: 0.7739 (t70) cc_final: 0.7416 (t0)
REVERT: C  102 TYR cc_start: 0.6944 (t80) cc_final: 0.6638 (t80)
REVERT: C  109 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7952 (ttm110)
REVERT: C  161 ASP cc_start: 0.7657 (p0) cc_final: 0.7400 (p0)
REVERT: E  176 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7502 (tt)
REVERT: E  252 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8499 (tpt)
  outliers start: 17
  outliers final: 7
  residues processed: 205
  average time/residue: 0.0899
  time to fit residues: 27.5275
Evaluate side-chains
  177 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain E residue   86 ASP
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  252 MET
Chi-restraints excluded: chain D residue  212 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 187 GLN
A 245 ASN
B 187 GLN
C  19 ASN
D 245 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.167692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.110623 restraints weight = 26667.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 4.73
r_work: 0.2758 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  13712  Z= 0.268
  Angle     :  0.652   8.201  18578  Z= 0.338
  Chirality :  0.047   0.151   2096
  Planarity :  0.005   0.046   2268
  Dihedral  : 20.736 174.937   2334
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.28 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.22), residues: 1553
  helix:  2.71 (0.21), residues: 519
  sheet: -0.88 (0.27), residues: 356
  loop : -1.48 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 189 
 TYR   0.022   0.002   TYR E 102 
 PHE   0.015   0.002   PHE C  37 
 TRP   0.010   0.002   TRP A  47 
 HIS   0.003   0.001   HIS E 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00672 /  0.27 (13712)
  covalent geometry    : angle       0.65244 /  0.34 (18578)
  hydrogen bonds       : bond        0.08920 /  6.02 (  579)
  hydrogen bonds       : angle       5.10520 /  3.60 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6633 (mm-30)
REVERT: A  122 ASP cc_start: 0.8783 (p0) cc_final: 0.8534 (p0)
REVERT: C   88 ASP cc_start: 0.7815 (t70) cc_final: 0.7549 (t0)
REVERT: C  102 TYR cc_start: 0.7018 (t80) cc_final: 0.6765 (t80)
  outliers start: 32
  outliers final: 25
  residues processed: 194
  average time/residue: 0.1166
  time to fit residues: 33.6610
Evaluate side-chains
  194 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  246 LEU
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  244 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 140 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 149 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  19 ASN
B  40 ASN
B 187 GLN
C  19 ASN
D  40 ASN
D 245 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.172206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114352 restraints weight = 19439.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.92
r_work: 0.2947 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.0830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13712  Z= 0.132
  Angle     :  0.536   7.888  18578  Z= 0.277
  Chirality :  0.043   0.158   2096
  Planarity :  0.004   0.043   2268
  Dihedral  : 19.602 171.276   2327
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.06 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.22), residues: 1553
  helix:  3.10 (0.21), residues: 519
  sheet: -0.55 (0.26), residues: 382
  loop : -1.43 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 109 
 TYR   0.013   0.001   TYR E 102 
 PHE   0.019   0.001   PHE C  37 
 TRP   0.008   0.001   TRP A 160 
 HIS   0.002   0.001   HIS D 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (13712)
  covalent geometry    : angle       0.53556 /  0.28 (18578)
  hydrogen bonds       : bond        0.06429 /  4.38 (  579)
  hydrogen bonds       : angle       4.51164 /  3.18 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.488 
Fit side-chains
REVERT: B  161 ASP cc_start: 0.8102 (p0) cc_final: 0.7820 (p0)
REVERT: C   88 ASP cc_start: 0.7857 (t70) cc_final: 0.7630 (t0)
REVERT: C  133 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6169 (ptm160)
REVERT: E  176 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8109 (tt)
  outliers start: 28
  outliers final: 19
  residues processed: 203
  average time/residue: 0.1090
  time to fit residues: 33.5866
Evaluate side-chains
  194 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 174
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  176 LEU
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain D residue   40 ASN
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  212 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 139 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 133 optimal weight:    0.9990
   chunk 129 optimal weight:   30.0000
   overall best weight:    2.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 187 GLN
C  19 ASN
E 173 ASN
D 245 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.168173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.110751 restraints weight = 25331.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 4.51
r_work: 0.2838 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13712  Z= 0.232
  Angle     :  0.611   8.432  18578  Z= 0.315
  Chirality :  0.045   0.153   2096
  Planarity :  0.004   0.049   2268
  Dihedral  : 19.607 171.250   2327
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.92 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.22), residues: 1553
  helix:  2.84 (0.21), residues: 519
  sheet: -0.55 (0.26), residues: 382
  loop : -1.52 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 189 
 TYR   0.026   0.002   TYR D 102 
 PHE   0.015   0.002   PHE C  37 
 TRP   0.009   0.002   TRP A  47 
 HIS   0.003   0.001   HIS B 127 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00580 /  0.23 (13712)
  covalent geometry    : angle       0.61098 /  0.32 (18578)
  hydrogen bonds       : bond        0.08208 /  5.56 (  579)
  hydrogen bonds       : angle       4.62162 /  3.25 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6437 (mm-30)
REVERT: A   33 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.5136 (mtmm)
REVERT: A  122 ASP cc_start: 0.8770 (p0) cc_final: 0.8533 (p0)
REVERT: C  102 TYR cc_start: 0.7047 (t80) cc_final: 0.6764 (t80)
REVERT: C  133 ARG cc_start: 0.6619 (ptm160) cc_final: 0.6321 (ptm160)
  outliers start: 43
  outliers final: 31
  residues processed: 200
  average time/residue: 0.1096
  time to fit residues: 32.9839
Evaluate side-chains
  207 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain D residue   40 ASN
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  244 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 154 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 63 optimal weight:    9.9990
   chunk 117 optimal weight:    5.9990
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 187 GLN
E 127 HIS
E 187 GLN
D  40 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.173570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.107656 restraints weight = 21154.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.78
r_work: 0.2966 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13712  Z= 0.111
  Angle     :  0.517   6.889  18578  Z= 0.267
  Chirality :  0.043   0.153   2096
  Planarity :  0.004   0.042   2268
  Dihedral  : 18.471 169.489   2327
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.13 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.22), residues: 1553
  helix:  3.23 (0.21), residues: 519
  sheet: -0.41 (0.27), residues: 389
  loop : -1.33 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.020   0.001   TYR D 102 
 PHE   0.011   0.001   PHE B 156 
 TRP   0.007   0.001   TRP A 160 
 HIS   0.002   0.001   HIS D 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 (13712)
  covalent geometry    : angle       0.51671 /  0.27 (18578)
  hydrogen bonds       : bond        0.05494 /  3.75 (  579)
  hydrogen bonds       : angle       4.18803 /  2.95 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.555 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6358 (mm-30)
REVERT: A  122 ASP cc_start: 0.8666 (p0) cc_final: 0.8422 (p0)
REVERT: B  161 ASP cc_start: 0.8031 (p0) cc_final: 0.7818 (p0)
REVERT: C  102 TYR cc_start: 0.6991 (t80) cc_final: 0.6708 (t80)
REVERT: C  133 ARG cc_start: 0.6491 (ptm160) cc_final: 0.6227 (ptm160)
REVERT: C  312 PHE cc_start: 0.7555 (m-10) cc_final: 0.7208 (t80)
  outliers start: 30
  outliers final: 17
  residues processed: 204
  average time/residue: 0.1094
  time to fit residues: 33.6996
Evaluate side-chains
  196 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  244 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 187 GLN
E 173 ASN
D  40 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.168320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.101288 restraints weight = 21148.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.78
r_work: 0.2900 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13712  Z= 0.221
  Angle     :  0.604   7.425  18578  Z= 0.311
  Chirality :  0.045   0.158   2096
  Planarity :  0.004   0.048   2268
  Dihedral  : 18.615 172.748   2326
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.28 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.22), residues: 1553
  helix:  2.90 (0.21), residues: 519
  sheet: -0.47 (0.27), residues: 382
  loop : -1.48 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.019   0.002   TYR D 102 
 PHE   0.015   0.001   PHE C  37 
 TRP   0.008   0.002   TRP A  47 
 HIS   0.002   0.001   HIS B 127 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00554 /  0.22 (13712)
  covalent geometry    : angle       0.60397 /  0.31 (18578)
  hydrogen bonds       : bond        0.08136 /  5.51 (  579)
  hydrogen bonds       : angle       4.48807 /  3.17 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6247 (mm-30)
REVERT: A   33 LYS cc_start: 0.5417 (OUTLIER) cc_final: 0.5037 (mtmm)
REVERT: B  161 ASP cc_start: 0.8136 (p0) cc_final: 0.7881 (p0)
REVERT: C  102 TYR cc_start: 0.7058 (t80) cc_final: 0.6745 (t80)
REVERT: C  133 ARG cc_start: 0.6579 (ptm160) cc_final: 0.6271 (ptm160)
  outliers start: 45
  outliers final: 32
  residues processed: 199
  average time/residue: 0.1086
  time to fit residues: 32.3429
Evaluate side-chains
  200 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  244 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 76 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 145 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 127 HIS
B 187 GLN
C  19 ASN
E 173 ASN
D  40 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117401 restraints weight = 28236.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 5.16
r_work: 0.2850 rms_B_bonded: 5.03 restraints_weight: 2.0000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13712  Z= 0.115
  Angle     :  0.531  11.774  18578  Z= 0.273
  Chirality :  0.043   0.169   2096
  Planarity :  0.004   0.043   2268
  Dihedral  : 17.754 172.536   2326
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.63 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.22), residues: 1553
  helix:  3.25 (0.21), residues: 519
  sheet: -0.46 (0.26), residues: 407
  loop : -1.24 (0.24), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.019   0.001   TYR D 102 
 PHE   0.012   0.001   PHE C  37 
 TRP   0.007   0.001   TRP A 160 
 HIS   0.002   0.001   HIS E 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 (13712)
  covalent geometry    : angle       0.53124 /  0.27 (18578)
  hydrogen bonds       : bond        0.05508 /  3.76 (  579)
  hydrogen bonds       : angle       4.11699 /  2.90 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6457 (mm-30)
REVERT: C   44 SER cc_start: 0.7421 (t) cc_final: 0.6704 (p)
REVERT: C  109 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8058 (ttm110)
REVERT: C  133 ARG cc_start: 0.6494 (ptm160) cc_final: 0.6201 (ptm160)
REVERT: C  312 PHE cc_start: 0.7643 (m-10) cc_final: 0.7193 (t80)
  outliers start: 32
  outliers final: 26
  residues processed: 202
  average time/residue: 0.0983
  time to fit residues: 30.1776
Evaluate side-chains
  200 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain E residue   27 CYS
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  158 THR
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain D residue   40 ASN
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  244 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 115 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   overall best weight:    3.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 187 GLN
C  19 ASN
E 173 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.166894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.099860 restraints weight = 22906.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.82
r_work: 0.2870 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  13712  Z= 0.287
  Angle     :  0.662   9.012  18578  Z= 0.340
  Chirality :  0.047   0.177   2096
  Planarity :  0.005   0.051   2268
  Dihedral  : 18.321 176.233   2326
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.49 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.22), residues: 1553
  helix:  2.76 (0.21), residues: 519
  sheet: -0.49 (0.27), residues: 382
  loop : -1.51 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 109 
 TYR   0.018   0.002   TYR D 102 
 PHE   0.019   0.002   PHE B  37 
 TRP   0.012   0.002   TRP E 213 
 HIS   0.003   0.001   HIS C 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00727 /  0.29 (13712)
  covalent geometry    : angle       0.66166 /  0.34 (18578)
  hydrogen bonds       : bond        0.09023 /  6.10 (  579)
  hydrogen bonds       : angle       4.57315 /  3.22 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 164
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6262 (mm-30)
REVERT: A   33 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.5111 (mtmm)
REVERT: C  102 TYR cc_start: 0.7121 (t80) cc_final: 0.6868 (t80)
REVERT: C  133 ARG cc_start: 0.6616 (ptm160) cc_final: 0.6296 (ptm160)
  outliers start: 44
  outliers final: 36
  residues processed: 192
  average time/residue: 0.1049
  time to fit residues: 30.5070
Evaluate side-chains
  198 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain E residue   27 CYS
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  158 THR
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  244 THR
Chi-restraints excluded: chain D residue  253 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0870
   chunk 60 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 86 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    0.7162

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 127 HIS
B 187 GLN
C  19 ASN
E 173 ASN
D  40 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.173017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.105922 restraints weight = 25705.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.04
r_work: 0.2899 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13712  Z= 0.115
  Angle     :  0.538   9.811  18578  Z= 0.276
  Chirality :  0.043   0.161   2096
  Planarity :  0.004   0.044   2268
  Dihedral  : 17.509 175.621   2326
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.63 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.22), residues: 1553
  helix:  3.23 (0.21), residues: 519
  sheet: -0.34 (0.27), residues: 389
  loop : -1.30 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.019   0.001   TYR D 102 
 PHE   0.012   0.001   PHE B 156 
 TRP   0.008   0.001   TRP E  47 
 HIS   0.002   0.001   HIS D 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 (13712)
  covalent geometry    : angle       0.53760 /  0.28 (18578)
  hydrogen bonds       : bond        0.05631 /  3.85 (  579)
  hydrogen bonds       : angle       4.14894 /  2.92 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6355 (mm-30)
REVERT: C   44 SER cc_start: 0.7258 (t) cc_final: 0.6527 (p)
REVERT: C  133 ARG cc_start: 0.6423 (ptm160) cc_final: 0.6132 (ptm160)
REVERT: C  312 PHE cc_start: 0.7573 (m-10) cc_final: 0.7179 (t80)
  outliers start: 30
  outliers final: 25
  residues processed: 195
  average time/residue: 0.1063
  time to fit residues: 31.3208
Evaluate side-chains
  199 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain E residue   27 CYS
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain D residue   40 ASN
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  169 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 65 optimal weight:    0.0040
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 54 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 141 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 146 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.5954

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 187 GLN
C  19 ASN
E 173 ASN
D  40 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.171450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.117052 restraints weight = 18800.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.91
r_work: 0.2907 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13712  Z= 0.149
  Angle     :  0.553   9.161  18578  Z= 0.284
  Chirality :  0.043   0.161   2096
  Planarity :  0.004   0.043   2268
  Dihedral  : 17.434 176.257   2326
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.63 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.22), residues: 1553
  helix:  3.17 (0.21), residues: 519
  sheet: -0.34 (0.27), residues: 389
  loop : -1.31 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 109 
 TYR   0.020   0.001   TYR D 102 
 PHE   0.014   0.001   PHE C  37 
 TRP   0.008   0.001   TRP A 160 
 HIS   0.002   0.001   HIS C 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 (13712)
  covalent geometry    : angle       0.55345 /  0.28 (18578)
  hydrogen bonds       : bond        0.06334 /  4.32 (  579)
  hydrogen bonds       : angle       4.17389 /  2.94 ( 1804)

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

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

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3106 Ramachandran restraints generated.
    1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   26 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6345 (mm-30)
REVERT: C   44 SER cc_start: 0.7291 (t) cc_final: 0.6554 (p)
REVERT: C  133 ARG cc_start: 0.6433 (ptm160) cc_final: 0.6133 (ptm160)
REVERT: E   23 TYR cc_start: 0.8628 (t80) cc_final: 0.8427 (t80)
  outliers start: 29
  outliers final: 28
  residues processed: 193
  average time/residue: 0.1022
  time to fit residues: 29.7998
Evaluate side-chains
  204 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   32 ASP
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain E residue   27 CYS
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain E residue  158 THR
Chi-restraints excluded: chain E residue  214 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain D residue   40 ASN
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  169 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 146 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 114 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0670
   chunk 127 optimal weight:    0.9990
   overall best weight:    1.1524

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 245 ASN
B 187 GLN
C  19 ASN
E 173 ASN
D  40 ASN
D 200 ASN
D 245 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.172358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.104648 restraints weight = 30189.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.22
r_work: 0.2866 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8767
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13712  Z= 0.128
  Angle     :  0.540   9.118  18578  Z= 0.278
  Chirality :  0.043   0.160   2096
  Planarity :  0.004   0.042   2268
  Dihedral  : 17.301 176.390   2326
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.35 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.22), residues: 1553
  helix:  3.20 (0.21), residues: 519
  sheet: -0.31 (0.27), residues: 389
  loop : -1.29 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  85 
 TYR   0.019   0.001   TYR D 102 
 PHE   0.013   0.001   PHE C  37 
 TRP   0.007   0.001   TRP A 160 
 HIS   0.002   0.001   HIS C 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 (13712)
  covalent geometry    : angle       0.54013 /  0.28 (18578)
  hydrogen bonds       : bond        0.06040 /  4.12 (  579)
  hydrogen bonds       : angle       4.14933 /  2.93 ( 1804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3454.50 seconds
wall clock time: 59 minutes 49.73 seconds (3589.73 seconds total)