Starting phenix.real_space_refine
on Thu Mar  6 09:03:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7td6_25824/03_2025/7td6_25824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7td6_25824/03_2025/7td6_25824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7td6_25824/03_2025/7td6_25824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7td6_25824/03_2025/7td6_25824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7td6_25824/03_2025/7td6_25824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7td6_25824/03_2025/7td6_25824.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    3460      2.51       5
     N    1010      2.21       5
     O    1060      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5575
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "1"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "A"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
  Time building chain proxies: 4.33, per 1000 atoms: 0.78
  Number of scatterers: 5575
  At special positions: 0
  Unit cell: (105.73, 112.27, 53.41, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1060      8.00
     N    1010      7.00
     C    3460      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS 1 178 " - pdb=" SG  CYS 1 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 178 " - pdb=" SG  CYS A 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 178 " - pdb=" SG  CYS B 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 178 " - pdb=" SG  CYS C 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 178 " - pdb=" SG  CYS D 213 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 664.9 milliseconds
  

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1270

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 13 sheets defined
      0.0% alpha, 40.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 94 through 99
      removed outlier: 6.507A  pdb=" N   THR 1  94 " --> pdb=" O   HIS B  95 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   GLN B  97 " --> pdb=" O   THR 1  94 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ASN 1  96 " --> pdb=" O   GLN B  97 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   ASN B  99 " --> pdb=" O   ASN 1  96 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP 1  98 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   HIS 1  95 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   TRP A  98 " --> pdb=" O   HIS 1  95 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   GLN 1  97 " --> pdb=" O   TRP A  98 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   HIS A  95 " --> pdb=" O   ASN C  96 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   TRP C  98 " --> pdb=" O   HIS A  95 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   GLN A  97 " --> pdb=" O   TRP C  98 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   HIS C  95 " --> pdb=" O   ASN D  96 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   TRP D  98 " --> pdb=" O   HIS C  95 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   GLN C  97 " --> pdb=" O   TRP D  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 112
      removed outlier: 7.125A  pdb=" N   HIS B 110 " --> pdb=" O   LYS 1 109 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL 1 111 " --> pdb=" O   HIS B 110 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ALA B 112 " --> pdb=" O   VAL 1 111 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   THR 1 106 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   LYS A 109 " --> pdb=" O   THR 1 106 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   LEU 1 108 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL A 111 " --> pdb=" O   LEU 1 108 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   HIS 1 110 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR A 106 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   LYS C 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 8.929A  pdb=" N   LEU A 108 " --> pdb=" O   LYS C 109 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   VAL C 111 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   HIS A 110 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   THR C 106 " --> pdb=" O   ASN D 107 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   LYS D 109 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 8.938A  pdb=" N   LEU C 108 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL D 111 " --> pdb=" O   LEU C 108 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   HIS C 110 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '1' and resid 120 through 121
    Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 134
      removed outlier: 6.336A  pdb=" N   MET 1 128 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   SER B 131 " --> pdb=" O   MET 1 128 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   GLY 1 130 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 10.502A  pdb=" N   MET B 133 " --> pdb=" O   GLY 1 130 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   ALA 1 132 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   SER 1 131 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ALA A 132 " --> pdb=" O   SER 1 131 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   MET 1 133 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   SER A 134 " --> pdb=" O   MET 1 133 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   SER A 131 " --> pdb=" O   GLY C 130 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ALA C 132 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   MET A 133 " --> pdb=" O   ALA C 132 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   SER C 134 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER C 131 " --> pdb=" O   GLY D 130 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ALA D 132 " --> pdb=" O   SER C 131 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   MET C 133 " --> pdb=" O   ALA D 132 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   SER D 134 " --> pdb=" O   MET C 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139
      removed outlier: 6.333A  pdb=" N   MET 1 137 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 143 through 144
      removed outlier: 6.516A  pdb=" N   ASP 1 143 " --> pdb=" O   TRP B 144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 155
      removed outlier: 6.812A  pdb=" N   TYR 1 154 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162
      removed outlier: 6.448A  pdb=" N   GLN 1 159 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   TYR A 162 " --> pdb=" O   GLN 1 159 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR 1 161 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLN A 159 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   TYR C 162 " --> pdb=" O   GLN A 159 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR A 161 " --> pdb=" O   TYR C 162 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLN C 159 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   TYR D 162 " --> pdb=" O   GLN C 159 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR C 161 " --> pdb=" O   TYR D 162 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 172
      removed outlier: 6.465A  pdb=" N   GLN 1 167 " --> pdb=" O   TYR B 168 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   ASN B 170 " --> pdb=" O   GLN 1 167 " (cutoff:3.500A)
      removed outlier: 9.008A  pdb=" N   SER 1 169 " --> pdb=" O   ASN B 170 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASN B 172 " --> pdb=" O   SER 1 169 " (cutoff:3.500A)
      removed outlier: 9.198A  pdb=" N   GLN 1 171 " --> pdb=" O   ASN B 172 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   GLN A 171 " --> pdb=" O   ASN 1 170 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASN 1 172 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   GLN C 171 " --> pdb=" O   ASN A 170 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ASN A 172 " --> pdb=" O   GLN C 171 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLN D 171 " --> pdb=" O   ASN C 170 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   ASN C 172 " --> pdb=" O   GLN D 171 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 189
      removed outlier: 6.899A  pdb=" N   ASN 1 180 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL 1 179 " --> pdb=" O   ASN A 180 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   THR A 182 " --> pdb=" O   VAL 1 179 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE 1 181 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LYS A 184 " --> pdb=" O   ILE 1 181 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ILE 1 183 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   HIS A 186 " --> pdb=" O   ILE 1 183 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLN 1 185 " --> pdb=" O   HIS A 186 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   VAL A 188 " --> pdb=" O   GLN 1 185 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   THR 1 187 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 179 " --> pdb=" O   ASN C 180 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   THR C 182 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE A 181 " --> pdb=" O   THR C 182 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   LYS C 184 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE A 183 " --> pdb=" O   LYS C 184 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   HIS C 186 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   GLN A 185 " --> pdb=" O   HIS C 186 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   VAL C 188 " --> pdb=" O   GLN A 185 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   THR A 187 " --> pdb=" O   VAL C 188 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL C 179 " --> pdb=" O   ASN D 180 " (cutoff:3.500A)
      removed outlier: 9.043A  pdb=" N   THR D 182 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ILE C 181 " --> pdb=" O   THR D 182 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   LYS D 184 " --> pdb=" O   ILE C 181 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE C 183 " --> pdb=" O   LYS D 184 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   HIS D 186 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   GLN C 185 " --> pdb=" O   HIS D 186 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   VAL D 188 " --> pdb=" O   GLN C 185 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   THR C 187 " --> pdb=" O   VAL D 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 206
      removed outlier: 6.238A  pdb=" N   GLU 1 199 " --> pdb=" O   THR A 200 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   VAL A 202 " --> pdb=" O   GLU 1 199 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASP 1 201 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   MET A 204 " --> pdb=" O   ASP 1 201 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LYS 1 203 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   GLU A 206 " --> pdb=" O   LYS 1 203 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   MET 1 205 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   GLU A 199 " --> pdb=" O   THR C 200 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   VAL C 202 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ASP A 201 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   MET C 204 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS A 203 " --> pdb=" O   MET C 204 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   GLU C 206 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   MET A 205 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   GLU C 199 " --> pdb=" O   THR D 200 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   VAL D 202 " --> pdb=" O   GLU C 199 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ASP C 201 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 218 through 219
      removed outlier: 6.374A  pdb=" N   GLN 1 218 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLN A 218 " --> pdb=" O   LYS C 219 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLN C 218 " --> pdb=" O   LYS D 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 225
      removed outlier: 6.275A  pdb=" N   ALA 1 223 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ALA A 223 " --> pdb=" O   TYR C 224 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ALA C 223 " --> pdb=" O   TYR D 224 " (cutoff:3.500A)

    65 hydrogen bonds defined for protein.
    195 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: 1.29

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1875
        1.34 -     1.46: 1337
        1.46 -     1.58: 2418
        1.58 -     1.70: 0
        1.70 -     1.81: 80
  Bond restraints: 5710
  Sorted by residual:
  bond pdb=" C   ASP B 166 "
       pdb=" N   GLN B 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.40e-02 5.10e+03 7.22e-01
  bond pdb=" C   ASP D 166 "
       pdb=" N   GLN D 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.40e-02 5.10e+03 7.19e-01
  bond pdb=" C   ASP C 166 "
       pdb=" N   GLN C 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.40e-02 5.10e+03 6.90e-01
  bond pdb=" C   ASP 1 166 "
       pdb=" N   GLN 1 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.341 -0.011 1.40e-02 5.10e+03 6.26e-01
  bond pdb=" C   ASP A 166 "
       pdb=" N   GLN A 167 "
    ideal  model  delta    sigma   weight residual
    1.330  1.341 -0.011 1.40e-02 5.10e+03 6.03e-01
  ... (remaining 5705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 7320
        1.07 -     2.14: 291
        2.14 -     3.20: 64
        3.20 -     4.27: 30
        4.27 -     5.34: 15
  Bond angle restraints: 7720
  Sorted by residual:
  angle pdb=" N   ASN B 180 "
        pdb=" CA  ASN B 180 "
        pdb=" C   ASN B 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.08   -4.80 1.35e+00 5.49e-01 1.26e+01
  angle pdb=" N   ASN A 180 "
        pdb=" CA  ASN A 180 "
        pdb=" C   ASN A 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.07   -4.79 1.35e+00 5.49e-01 1.26e+01
  angle pdb=" N   ASN 1 180 "
        pdb=" CA  ASN 1 180 "
        pdb=" C   ASN 1 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.04   -4.76 1.35e+00 5.49e-01 1.24e+01
  angle pdb=" N   ASN D 180 "
        pdb=" CA  ASN D 180 "
        pdb=" C   ASN D 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.04   -4.76 1.35e+00 5.49e-01 1.24e+01
  angle pdb=" N   ASN C 180 "
        pdb=" CA  ASN C 180 "
        pdb=" C   ASN C 180 "
      ideal   model   delta    sigma   weight residual
     111.28  116.01   -4.73 1.35e+00 5.49e-01 1.23e+01
  ... (remaining 7715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.38: 2946
       15.38 -    30.77: 279
       30.77 -    46.15: 110
       46.15 -    61.53: 40
       61.53 -    76.92: 25
  Dihedral angle restraints: 3400
    sinusoidal: 1390
      harmonic: 2010
  Sorted by residual:
  dihedral pdb=" CA  ASP A 201 "
           pdb=" CB  ASP A 201 "
           pdb=" CG  ASP A 201 "
           pdb=" OD1 ASP A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.89   51.89     1      2.00e+01 2.50e-03 9.19e+00
  dihedral pdb=" CA  ASP C 201 "
           pdb=" CB  ASP C 201 "
           pdb=" CG  ASP C 201 "
           pdb=" OD1 ASP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.87   51.87     1      2.00e+01 2.50e-03 9.18e+00
  dihedral pdb=" CA  ASP 1 201 "
           pdb=" CB  ASP 1 201 "
           pdb=" CG  ASP 1 201 "
           pdb=" OD1 ASP 1 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.87   51.87     1      2.00e+01 2.50e-03 9.18e+00
  ... (remaining 3397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 516
       0.036 -    0.072: 147
       0.072 -    0.108: 86
       0.108 -    0.145: 26
       0.145 -    0.181: 5
  Chirality restraints: 780
  Sorted by residual:
  chirality pdb=" CA  ASN B 180 "
            pdb=" N   ASN B 180 "
            pdb=" C   ASN B 180 "
            pdb=" CB  ASN B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.16e-01
  chirality pdb=" CA  ASN A 180 "
            pdb=" N   ASN A 180 "
            pdb=" C   ASN A 180 "
            pdb=" CB  ASN A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CA  ASN 1 180 "
            pdb=" N   ASN 1 180 "
            pdb=" C   ASN 1 180 "
            pdb=" CB  ASN 1 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.77e-01
  ... (remaining 777 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 217 "   -0.005 2.00e-02 2.50e+03   4.37e-03 3.82e-01
        pdb=" CG  TYR D 217 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 217 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D 217 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 217 "   -0.006 2.00e-02 2.50e+03   4.33e-03 3.75e-01
        pdb=" CG  TYR B 217 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 217 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 217 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR 1 217 "   -0.006 2.00e-02 2.50e+03   4.31e-03 3.71e-01
        pdb=" CG  TYR 1 217 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR 1 217 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR 1 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR 1 217 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR 1 217 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR 1 217 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR 1 217 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 2165
        2.94 -     3.43: 5104
        3.43 -     3.92: 9900
        3.92 -     4.41: 10113
        4.41 -     4.90: 18108
  Nonbonded interactions: 45390
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 145 "
            pdb=" NH2 ARG B 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU C 145 "
            pdb=" NH2 ARG C 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU 1 145 "
            pdb=" NH2 ARG 1 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU A 145 "
            pdb=" NH2 ARG A 150 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE1 GLU D 145 "
            pdb=" NH2 ARG D 150 "
     model   vdw
     2.450 3.120
  ... (remaining 45385 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain '1'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.690
  Find NCS groups from input model:        0.110
  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:11.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
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      :  0.002   0.020   5710  Z= 0.126
  Angle     :  0.570   5.341   7720  Z= 0.350
  Chirality :  0.049   0.181    780
  Planarity :  0.001   0.012   1020
  Dihedral  : 16.473  76.917   2115
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.27), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 144 
 HIS   0.001   0.000   HIS A 110 
 PHE   0.009   0.001   PHE B 174 
 TYR   0.010   0.001   TYR B 217 
 ARG   0.001   0.000   ARG C 155 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.652 
Fit side-chains
REVERT: 1  153 MET cc_start: 0.7616 (mmm) cc_final: 0.7408 (mmm)
REVERT: 1  220 GLU cc_start: 0.8457 (mp0) cc_final: 0.7958 (mp0)
REVERT: 1  226 ASP cc_start: 0.7652 (m-30) cc_final: 0.7089 (p0)
REVERT: A  224 TYR cc_start: 0.7614 (m-80) cc_final: 0.7379 (m-80)
REVERT: B  151 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7071 (pm20)
REVERT: B  155 ARG cc_start: 0.7969 (mtt180) cc_final: 0.6605 (mmp-170)
REVERT: B  163 ARG cc_start: 0.8144 (mtt180) cc_final: 0.6928 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8551 (t) cc_final: 0.8148 (m)
REVERT: B  199 GLU cc_start: 0.8007 (mp0) cc_final: 0.7556 (mp0)
REVERT: B  207 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6030 (ppt90)
REVERT: B  212 MET cc_start: 0.8166 (tpp) cc_final: 0.7840 (ttm)
REVERT: B  219 LYS cc_start: 0.8094 (mttt) cc_final: 0.6418 (pmtt)
REVERT: B  220 GLU cc_start: 0.8054 (mp0) cc_final: 0.7338 (pp20)
REVERT: B  221 SER cc_start: 0.8904 (m) cc_final: 0.8403 (m)
REVERT: C  128 MET cc_start: 0.8796 (mtp) cc_final: 0.8456 (mtp)
REVERT: C  155 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7245 (mtp85)
REVERT: C  215 THR cc_start: 0.8787 (m) cc_final: 0.8521 (t)
REVERT: C  220 GLU cc_start: 0.8455 (mp0) cc_final: 0.8002 (mp0)
REVERT: C  226 ASP cc_start: 0.7721 (m-30) cc_final: 0.7145 (p0)
REVERT: D  100 LYS cc_start: 0.7426 (mtmt) cc_final: 0.6745 (mmtt)
REVERT: D  135 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7247 (tpm170)
REVERT: D  140 PHE cc_start: 0.7749 (m-80) cc_final: 0.6770 (p90)
REVERT: D  143 ASP cc_start: 0.8149 (t0) cc_final: 0.7946 (m-30)
REVERT: D  153 MET cc_start: 0.8006 (mmm) cc_final: 0.6871 (ptt)
REVERT: D  155 ARG cc_start: 0.7800 (mtt180) cc_final: 0.6756 (ptt-90)
REVERT: D  163 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7261 (pmt170)
REVERT: D  207 ARG cc_start: 0.7603 (mtt180) cc_final: 0.6783 (mmp-170)
REVERT: D  212 MET cc_start: 0.8244 (tpp) cc_final: 0.6896 (pmt)
REVERT: D  217 TYR cc_start: 0.8499 (p90) cc_final: 0.7999 (p90)
REVERT: D  219 LYS cc_start: 0.8071 (mttt) cc_final: 0.7761 (mmtt)
REVERT: D  222 GLN cc_start: 0.8555 (mp-120) cc_final: 0.8158 (mp10)
REVERT: D  224 TYR cc_start: 0.7638 (m-80) cc_final: 0.7131 (m-80)
REVERT: D  229 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7277 (pmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 1.5259
  time to fit residues: 314.9396
Evaluate side-chains
  155 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0000
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    8.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
1 158 ASN
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
A 158 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
B 158 ASN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
C 158 ASN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
D 173 ASN
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.118301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.103396 restraints weight = 10081.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 2.86
r_work: 0.3976 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5710  Z= 0.219
  Angle     :  0.597   6.478   7720  Z= 0.323
  Chirality :  0.047   0.132    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  4.600  16.761    780
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.45 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.26), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 144 
 HIS   0.003   0.001   HIS D 186 
 PHE   0.016   0.003   PHE B 197 
 TYR   0.026   0.002   TYR C 217 
 ARG   0.004   0.000   ARG A 135 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.633 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8513 (ptm-80) cc_final: 0.8276 (ptp90)
REVERT: 1  137 MET cc_start: 0.8467 (ttm) cc_final: 0.7994 (ttm)
REVERT: 1  153 MET cc_start: 0.7761 (mmm) cc_final: 0.7489 (mmm)
REVERT: 1  219 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7693 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8613 (mp0) cc_final: 0.8110 (mp0)
REVERT: A  135 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.8171 (ptp90)
REVERT: A  145 GLU cc_start: 0.8361 (mp0) cc_final: 0.8116 (mp0)
REVERT: A  197 PHE cc_start: 0.6788 (m-10) cc_final: 0.5813 (m-80)
REVERT: A  204 MET cc_start: 0.6701 (tmm) cc_final: 0.6395 (tmm)
REVERT: A  229 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7957 (mmt-90)
REVERT: B  135 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.4760 (pmt170)
REVERT: B  151 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7029 (pm20)
REVERT: B  155 ARG cc_start: 0.8451 (mtt180) cc_final: 0.6778 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8705 (t) cc_final: 0.8290 (m)
REVERT: B  212 MET cc_start: 0.8645 (tpp) cc_final: 0.8382 (ttm)
REVERT: B  219 LYS cc_start: 0.8181 (mttt) cc_final: 0.6597 (pmtt)
REVERT: B  220 GLU cc_start: 0.8291 (mp0) cc_final: 0.7543 (pp20)
REVERT: B  221 SER cc_start: 0.8914 (m) cc_final: 0.8457 (m)
REVERT: C  128 MET cc_start: 0.9117 (mtp) cc_final: 0.8887 (mtp)
REVERT: C  137 MET cc_start: 0.8381 (ttm) cc_final: 0.7982 (ttm)
REVERT: C  155 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7709 (mtp85)
REVERT: C  204 MET cc_start: 0.6791 (tmt) cc_final: 0.6350 (tmt)
REVERT: C  220 GLU cc_start: 0.8542 (mp0) cc_final: 0.8316 (mp0)
REVERT: D  100 LYS cc_start: 0.7465 (mtmt) cc_final: 0.6733 (mmtt)
REVERT: D  133 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6790 (mpt)
REVERT: D  135 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7336 (tpm170)
REVERT: D  140 PHE cc_start: 0.7958 (m-80) cc_final: 0.6709 (p90)
REVERT: D  143 ASP cc_start: 0.8474 (t0) cc_final: 0.7994 (m-30)
REVERT: D  153 MET cc_start: 0.8351 (mmm) cc_final: 0.6938 (ptt)
REVERT: D  155 ARG cc_start: 0.8269 (mtt180) cc_final: 0.6762 (ptt-90)
REVERT: D  163 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7290 (pmt170)
REVERT: D  177 ASP cc_start: 0.7882 (m-30) cc_final: 0.7488 (m-30)
REVERT: D  204 MET cc_start: 0.6914 (tmm) cc_final: 0.6636 (tmm)
REVERT: D  206 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7167 (tm-30)
REVERT: D  207 ARG cc_start: 0.8001 (mtt180) cc_final: 0.6513 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8221 (mm-40)
REVERT: D  212 MET cc_start: 0.8689 (tpp) cc_final: 0.6965 (pmt)
REVERT: D  222 GLN cc_start: 0.8683 (mp-120) cc_final: 0.8282 (mp10)
REVERT: D  224 TYR cc_start: 0.7984 (m-80) cc_final: 0.7573 (m-80)
REVERT: D  226 ASP cc_start: 0.7469 (p0) cc_final: 0.7020 (p0)
REVERT: D  229 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7174 (pmt170)
  outliers start: 13
  outliers final: 3
  residues processed: 168
  average time/residue: 1.3637
  time to fit residues: 237.4356
Evaluate side-chains
  163 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.115591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.099884 restraints weight = 9995.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 2.98
r_work: 0.3935 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5710  Z= 0.287
  Angle     :  0.633   7.999   7720  Z= 0.340
  Chirality :  0.048   0.136    780
  Planarity :  0.003   0.022   1020
  Dihedral  :  5.209  18.685    780
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.64 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.26), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.014   0.003   PHE B 174 
 TYR   0.028   0.002   TYR C 217 
 ARG   0.003   0.000   ARG C 135 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 0.565 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.7970 (ptp90)
REVERT: 1  137 MET cc_start: 0.8151 (ttm) cc_final: 0.7731 (ttm)
REVERT: 1  153 MET cc_start: 0.7614 (mmm) cc_final: 0.7222 (mmm)
REVERT: 1  197 PHE cc_start: 0.6715 (m-10) cc_final: 0.6482 (m-10)
REVERT: 1  204 MET cc_start: 0.6241 (tmm) cc_final: 0.5760 (tmt)
REVERT: 1  205 MET cc_start: 0.8878 (ttm) cc_final: 0.8367 (mtm)
REVERT: 1  219 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7681 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8619 (mp0) cc_final: 0.8171 (mp0)
REVERT: A  145 GLU cc_start: 0.8433 (mp0) cc_final: 0.8127 (mp0)
REVERT: A  161 TYR cc_start: 0.8849 (m-10) cc_final: 0.8564 (m-80)
REVERT: A  211 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7650 (mt0)
REVERT: B  100 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7974 (mttp)
REVERT: B  155 ARG cc_start: 0.8003 (mtt180) cc_final: 0.6344 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8257 (tp30) cc_final: 0.7381 (tm-30)
REVERT: B  207 ARG cc_start: 0.7574 (mtt180) cc_final: 0.5742 (tmm160)
REVERT: B  212 MET cc_start: 0.8467 (tpp) cc_final: 0.8206 (ttm)
REVERT: B  219 LYS cc_start: 0.8098 (mttt) cc_final: 0.6659 (pmtt)
REVERT: B  220 GLU cc_start: 0.8325 (mp0) cc_final: 0.7506 (pp20)
REVERT: B  228 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.5960 (pmt-80)
REVERT: C  100 LYS cc_start: 0.7481 (mtmt) cc_final: 0.7161 (mttp)
REVERT: C  128 MET cc_start: 0.9098 (mtp) cc_final: 0.8789 (mtp)
REVERT: C  137 MET cc_start: 0.8060 (ttm) cc_final: 0.7573 (ttm)
REVERT: C  155 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7140 (mtt90)
REVERT: C  195 GLU cc_start: 0.5015 (tm-30) cc_final: 0.3999 (tt0)
REVERT: C  204 MET cc_start: 0.6320 (tmt) cc_final: 0.6005 (tmt)
REVERT: C  220 GLU cc_start: 0.8650 (mp0) cc_final: 0.8150 (mp0)
REVERT: D  100 LYS cc_start: 0.7446 (mtmt) cc_final: 0.6619 (mmtt)
REVERT: D  135 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6975 (tpm170)
REVERT: D  140 PHE cc_start: 0.8195 (m-80) cc_final: 0.6531 (p90)
REVERT: D  143 ASP cc_start: 0.8214 (t0) cc_final: 0.7798 (m-30)
REVERT: D  146 ASP cc_start: 0.8054 (t0) cc_final: 0.7791 (t0)
REVERT: D  155 ARG cc_start: 0.8299 (mtt180) cc_final: 0.6733 (ptt90)
REVERT: D  158 ASN cc_start: 0.8684 (m110) cc_final: 0.8420 (m-40)
REVERT: D  163 ARG cc_start: 0.8524 (mtt180) cc_final: 0.6955 (pmt170)
REVERT: D  204 MET cc_start: 0.6561 (tmm) cc_final: 0.6263 (tmm)
REVERT: D  207 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6044 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7748 (mm-40)
REVERT: D  212 MET cc_start: 0.8922 (tpp) cc_final: 0.6942 (pmt)
REVERT: D  221 SER cc_start: 0.8723 (p) cc_final: 0.8101 (m)
REVERT: D  222 GLN cc_start: 0.8357 (mp-120) cc_final: 0.7610 (mm-40)
REVERT: D  224 TYR cc_start: 0.7711 (m-80) cc_final: 0.7357 (m-80)
REVERT: D  229 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7059 (pmt170)
  outliers start: 15
  outliers final: 5
  residues processed: 178
  average time/residue: 1.3922
  time to fit residues: 256.3403
Evaluate side-chains
  161 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 154
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 54 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.115303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.099486 restraints weight = 10019.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 3.05
r_work: 0.3929 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5710  Z= 0.227
  Angle     :  0.617   7.596   7720  Z= 0.331
  Chirality :  0.048   0.132    780
  Planarity :  0.002   0.019   1020
  Dihedral  :  5.218  18.786    780
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.33 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.26), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP 1  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.014   0.002   PHE B 197 
 TYR   0.028   0.002   TYR C 217 
 ARG   0.004   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.664 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8311 (ptm-80) cc_final: 0.8009 (ptp90)
REVERT: 1  137 MET cc_start: 0.8229 (ttm) cc_final: 0.7904 (ttm)
REVERT: 1  153 MET cc_start: 0.7670 (mmm) cc_final: 0.7292 (mmm)
REVERT: 1  204 MET cc_start: 0.6098 (tmm) cc_final: 0.5727 (tmt)
REVERT: 1  205 MET cc_start: 0.8776 (ttm) cc_final: 0.8378 (mtm)
REVERT: 1  211 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (mm-40)
REVERT: 1  219 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7713 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8592 (mp0) cc_final: 0.8096 (mp0)
REVERT: A  133 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7515 (mtm)
REVERT: A  145 GLU cc_start: 0.8401 (mp0) cc_final: 0.8009 (mp0)
REVERT: A  161 TYR cc_start: 0.8864 (m-10) cc_final: 0.8503 (m-80)
REVERT: A  210 GLU cc_start: 0.7692 (mp0) cc_final: 0.7118 (mp0)
REVERT: A  211 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7942 (mt0)
REVERT: A  220 GLU cc_start: 0.8362 (mp0) cc_final: 0.8027 (mp0)
REVERT: B  100 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7886 (mttp)
REVERT: B  135 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.4814 (pmt170)
REVERT: B  145 GLU cc_start: 0.8285 (mp0) cc_final: 0.8080 (mp0)
REVERT: B  146 ASP cc_start: 0.8279 (t0) cc_final: 0.7959 (t0)
REVERT: B  155 ARG cc_start: 0.7985 (mtt180) cc_final: 0.6347 (mmp-170)
REVERT: B  161 TYR cc_start: 0.8366 (m-10) cc_final: 0.8036 (m-10)
REVERT: B  175 VAL cc_start: 0.8651 (t) cc_final: 0.8199 (m)
REVERT: B  212 MET cc_start: 0.8459 (tpp) cc_final: 0.8175 (ttm)
REVERT: B  219 LYS cc_start: 0.8087 (mttt) cc_final: 0.6511 (pmtt)
REVERT: B  220 GLU cc_start: 0.8347 (mp0) cc_final: 0.7530 (pp20)
REVERT: B  228 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.5948 (pmt-80)
REVERT: C  100 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7319 (mttp)
REVERT: C  128 MET cc_start: 0.9093 (mtp) cc_final: 0.8790 (mtp)
REVERT: C  137 MET cc_start: 0.8078 (ttm) cc_final: 0.7597 (ttm)
REVERT: C  155 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7188 (mtt90)
REVERT: C  195 GLU cc_start: 0.4938 (tm-30) cc_final: 0.3698 (tt0)
REVERT: C  204 MET cc_start: 0.6357 (tmt) cc_final: 0.5988 (tmt)
REVERT: C  210 GLU cc_start: 0.7621 (mp0) cc_final: 0.6921 (tm-30)
REVERT: C  220 GLU cc_start: 0.8727 (mp0) cc_final: 0.8313 (mp0)
REVERT: D  100 LYS cc_start: 0.7496 (mtmt) cc_final: 0.6621 (mmtt)
REVERT: D  135 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7008 (tpm170)
REVERT: D  140 PHE cc_start: 0.8254 (m-80) cc_final: 0.6359 (p90)
REVERT: D  143 ASP cc_start: 0.8246 (t0) cc_final: 0.7828 (m-30)
REVERT: D  145 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7859 (mt-10)
REVERT: D  146 ASP cc_start: 0.8005 (t0) cc_final: 0.7708 (t0)
REVERT: D  153 MET cc_start: 0.8615 (mmm) cc_final: 0.6603 (pp-130)
REVERT: D  155 ARG cc_start: 0.8244 (mtt180) cc_final: 0.6730 (ptt90)
REVERT: D  158 ASN cc_start: 0.8694 (m110) cc_final: 0.8438 (m-40)
REVERT: D  163 ARG cc_start: 0.8657 (mtt180) cc_final: 0.6982 (pmt170)
REVERT: D  167 GLN cc_start: 0.8843 (tt0) cc_final: 0.8587 (tt0)
REVERT: D  204 MET cc_start: 0.6491 (tmm) cc_final: 0.6180 (tmm)
REVERT: D  207 ARG cc_start: 0.8052 (mtt180) cc_final: 0.5955 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7720 (mm-40)
REVERT: D  212 MET cc_start: 0.8833 (tpp) cc_final: 0.6930 (pmt)
REVERT: D  221 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8450 (m)
REVERT: D  222 GLN cc_start: 0.8403 (mp-120) cc_final: 0.8019 (mp10)
REVERT: D  224 TYR cc_start: 0.7751 (m-80) cc_final: 0.7376 (m-80)
REVERT: D  229 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7041 (pmt170)
  outliers start: 24
  outliers final: 7
  residues processed: 176
  average time/residue: 1.4177
  time to fit residues: 258.1551
Evaluate side-chains
  162 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
B 142 ASN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.114197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.098613 restraints weight = 9905.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.92
r_work: 0.3912 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5710  Z= 0.292
  Angle     :  0.650   7.741   7720  Z= 0.349
  Chirality :  0.048   0.134    780
  Planarity :  0.003   0.018   1020
  Dihedral  :  5.435  19.242    780
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 20.00 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.023   0.003   PHE B 197 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.004   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.619 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.7984 (ptp90)
REVERT: 1  137 MET cc_start: 0.8144 (ttm) cc_final: 0.7793 (ttm)
REVERT: 1  153 MET cc_start: 0.7624 (mmm) cc_final: 0.7257 (mmm)
REVERT: 1  204 MET cc_start: 0.6036 (tmm) cc_final: 0.5642 (tmt)
REVERT: 1  205 MET cc_start: 0.8794 (ttm) cc_final: 0.8363 (mtm)
REVERT: 1  211 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8478 (mm-40)
REVERT: 1  212 MET cc_start: 0.8500 (tpp) cc_final: 0.8288 (ttm)
REVERT: 1  220 GLU cc_start: 0.8553 (mp0) cc_final: 0.8286 (mp0)
REVERT: A  133 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7375 (mtm)
REVERT: A  145 GLU cc_start: 0.8370 (mp0) cc_final: 0.7930 (mp0)
REVERT: A  155 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6962 (mpp80)
REVERT: A  197 PHE cc_start: 0.6075 (m-10) cc_final: 0.5254 (m-10)
REVERT: A  210 GLU cc_start: 0.7782 (mp0) cc_final: 0.7143 (mp0)
REVERT: A  211 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7682 (mt0)
REVERT: A  226 ASP cc_start: 0.7310 (p0) cc_final: 0.7066 (p0)
REVERT: B  100 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7715 (mttp)
REVERT: B  135 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.4788 (pmt170)
REVERT: B  140 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7185 (m-10)
REVERT: B  145 GLU cc_start: 0.8295 (mp0) cc_final: 0.8050 (mp0)
REVERT: B  146 ASP cc_start: 0.8193 (t0) cc_final: 0.7806 (t0)
REVERT: B  155 ARG cc_start: 0.7864 (mtt180) cc_final: 0.6230 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7071 (tm-30)
REVERT: B  207 ARG cc_start: 0.7756 (mtt180) cc_final: 0.5692 (tmm160)
REVERT: B  212 MET cc_start: 0.8369 (tpp) cc_final: 0.8083 (ttm)
REVERT: B  219 LYS cc_start: 0.8102 (mttt) cc_final: 0.6388 (pmtt)
REVERT: B  220 GLU cc_start: 0.8301 (mp0) cc_final: 0.7507 (pp20)
REVERT: B  228 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.5861 (pmt-80)
REVERT: C  100 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7040 (mttp)
REVERT: C  128 MET cc_start: 0.9062 (mtp) cc_final: 0.8775 (mtp)
REVERT: C  137 MET cc_start: 0.8011 (ttm) cc_final: 0.7576 (ttm)
REVERT: C  204 MET cc_start: 0.6328 (tmt) cc_final: 0.5988 (tmt)
REVERT: C  210 GLU cc_start: 0.7310 (mp0) cc_final: 0.6917 (tm-30)
REVERT: C  220 GLU cc_start: 0.8736 (mp0) cc_final: 0.8117 (mp0)
REVERT: D  100 LYS cc_start: 0.7463 (mtmt) cc_final: 0.6555 (mmtt)
REVERT: D  133 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6611 (mpt)
REVERT: D  135 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7142 (tpm170)
REVERT: D  140 PHE cc_start: 0.8334 (m-80) cc_final: 0.6365 (p90)
REVERT: D  143 ASP cc_start: 0.8151 (t0) cc_final: 0.7695 (m-30)
REVERT: D  145 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7884 (mt-10)
REVERT: D  146 ASP cc_start: 0.8114 (t0) cc_final: 0.7776 (t0)
REVERT: D  153 MET cc_start: 0.8637 (mmm) cc_final: 0.6674 (pp-130)
REVERT: D  155 ARG cc_start: 0.8222 (mtt180) cc_final: 0.6707 (ptt90)
REVERT: D  158 ASN cc_start: 0.8654 (m110) cc_final: 0.8366 (m-40)
REVERT: D  163 ARG cc_start: 0.8723 (mtt180) cc_final: 0.6973 (pmt170)
REVERT: D  204 MET cc_start: 0.6410 (tmm) cc_final: 0.6090 (tmm)
REVERT: D  207 ARG cc_start: 0.8058 (mtt180) cc_final: 0.5898 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7684 (mm-40)
REVERT: D  212 MET cc_start: 0.8822 (tpp) cc_final: 0.6939 (pmt)
REVERT: D  221 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8434 (m)
REVERT: D  222 GLN cc_start: 0.8303 (mp-120) cc_final: 0.7962 (mp-120)
REVERT: D  224 TYR cc_start: 0.7644 (m-80) cc_final: 0.7216 (m-80)
REVERT: D  229 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7032 (pmt170)
  outliers start: 23
  outliers final: 7
  residues processed: 168
  average time/residue: 1.5001
  time to fit residues: 260.3539
Evaluate side-chains
  167 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.113766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.098354 restraints weight = 9832.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 2.94
r_work: 0.3951 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5710  Z= 0.273
  Angle     :  0.656   7.621   7720  Z= 0.350
  Chirality :  0.048   0.133    780
  Planarity :  0.002   0.018   1020
  Dihedral  :  5.460  19.781    780
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.17 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.013   0.002   PHE 1 174 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.003   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.602 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8508 (ttm) cc_final: 0.8261 (ttm)
REVERT: 1  153 MET cc_start: 0.8090 (mmm) cc_final: 0.7811 (mmm)
REVERT: 1  204 MET cc_start: 0.6678 (tmm) cc_final: 0.6268 (tmt)
REVERT: 1  211 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8717 (mm-40)
REVERT: A  133 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7782 (mtm)
REVERT: A  145 GLU cc_start: 0.8545 (mp0) cc_final: 0.8213 (mp0)
REVERT: A  155 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7616 (mpp80)
REVERT: A  210 GLU cc_start: 0.8031 (mp0) cc_final: 0.7708 (mp0)
REVERT: A  211 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8176 (mt0)
REVERT: B  100 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8085 (mttp)
REVERT: B  140 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.7067 (m-10)
REVERT: B  155 ARG cc_start: 0.8432 (mtt180) cc_final: 0.6890 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: B  207 ARG cc_start: 0.7972 (mtt180) cc_final: 0.5981 (tmm160)
REVERT: B  212 MET cc_start: 0.8582 (tpp) cc_final: 0.8292 (ttm)
REVERT: B  219 LYS cc_start: 0.8279 (mttt) cc_final: 0.6687 (pmtt)
REVERT: B  220 GLU cc_start: 0.8294 (mp0) cc_final: 0.7609 (pp20)
REVERT: B  228 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.6161 (pmt-80)
REVERT: C  137 MET cc_start: 0.8486 (ttm) cc_final: 0.8145 (ttm)
REVERT: C  195 GLU cc_start: 0.5184 (tm-30) cc_final: 0.3974 (tt0)
REVERT: C  204 MET cc_start: 0.6851 (tmt) cc_final: 0.6528 (tmt)
REVERT: C  220 GLU cc_start: 0.8859 (mp0) cc_final: 0.8425 (mp0)
REVERT: D  100 LYS cc_start: 0.7822 (mtmt) cc_final: 0.6927 (mmtt)
REVERT: D  133 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7117 (mpt)
REVERT: D  135 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7718 (tpm170)
REVERT: D  140 PHE cc_start: 0.8186 (m-80) cc_final: 0.6312 (p90)
REVERT: D  143 ASP cc_start: 0.8277 (t0) cc_final: 0.8060 (m-30)
REVERT: D  145 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8149 (mt-10)
REVERT: D  146 ASP cc_start: 0.8465 (t0) cc_final: 0.8104 (t0)
REVERT: D  153 MET cc_start: 0.8642 (mmm) cc_final: 0.6696 (pp-130)
REVERT: D  155 ARG cc_start: 0.8394 (mtt180) cc_final: 0.7183 (ptt90)
REVERT: D  163 ARG cc_start: 0.8832 (mtt180) cc_final: 0.7231 (pmt170)
REVERT: D  207 ARG cc_start: 0.8390 (mtt180) cc_final: 0.6232 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8374 (mm-40)
REVERT: D  212 MET cc_start: 0.8701 (tpp) cc_final: 0.7114 (pmt)
REVERT: D  222 GLN cc_start: 0.8817 (mp-120) cc_final: 0.8509 (mp-120)
REVERT: D  224 TYR cc_start: 0.8244 (m-80) cc_final: 0.7989 (m-80)
REVERT: D  229 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7199 (pmt170)
  outliers start: 21
  outliers final: 8
  residues processed: 166
  average time/residue: 1.5019
  time to fit residues: 257.4989
Evaluate side-chains
  164 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0570
   chunk 48 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0870
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   overall best weight:    1.9880

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.114259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.098508 restraints weight = 9829.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.4095 rms_B_bonded: 2.97
r_work: 0.3957 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5710  Z= 0.246
  Angle     :  0.685   7.783   7720  Z= 0.367
  Chirality :  0.049   0.171    780
  Planarity :  0.003   0.021   1020
  Dihedral  :  5.474  20.518    780
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.67 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.017   0.003   PHE 1 197 
 TYR   0.030   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.664 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8474 (ttm) cc_final: 0.8172 (ttm)
REVERT: 1  153 MET cc_start: 0.8102 (mmm) cc_final: 0.7827 (mmm)
REVERT: 1  204 MET cc_start: 0.6647 (tmm) cc_final: 0.6259 (tmt)
REVERT: 1  205 MET cc_start: 0.8978 (ttm) cc_final: 0.8757 (mtm)
REVERT: 1  212 MET cc_start: 0.8659 (tpp) cc_final: 0.8416 (ttm)
REVERT: A  133 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7748 (mtm)
REVERT: A  145 GLU cc_start: 0.8577 (mp0) cc_final: 0.8277 (mp0)
REVERT: A  155 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7592 (mpp80)
REVERT: A  197 PHE cc_start: 0.6382 (m-10) cc_final: 0.6091 (m-10)
REVERT: B  100 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8037 (mttp)
REVERT: B  140 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.7022 (m-10)
REVERT: B  155 ARG cc_start: 0.8415 (mtt180) cc_final: 0.6811 (mmp-170)
REVERT: B  175 VAL cc_start: 0.9061 (t) cc_final: 0.8713 (m)
REVERT: B  206 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: B  207 ARG cc_start: 0.7951 (mtt180) cc_final: 0.5996 (tmm160)
REVERT: B  212 MET cc_start: 0.8599 (tpp) cc_final: 0.8347 (ttm)
REVERT: B  219 LYS cc_start: 0.8253 (mttt) cc_final: 0.6723 (pmtt)
REVERT: B  220 GLU cc_start: 0.8265 (mp0) cc_final: 0.7644 (pp20)
REVERT: B  228 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.6183 (pmt-80)
REVERT: C  137 MET cc_start: 0.8447 (ttm) cc_final: 0.8086 (ttm)
REVERT: C  161 TYR cc_start: 0.9228 (m-10) cc_final: 0.8837 (m-80)
REVERT: C  195 GLU cc_start: 0.5133 (tm-30) cc_final: 0.4424 (tt0)
REVERT: C  204 MET cc_start: 0.6823 (tmt) cc_final: 0.6480 (tmt)
REVERT: C  220 GLU cc_start: 0.8889 (mp0) cc_final: 0.8411 (mp0)
REVERT: D  100 LYS cc_start: 0.7803 (mtmt) cc_final: 0.6883 (mmtt)
REVERT: D  133 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7064 (mpt)
REVERT: D  135 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7670 (tpm170)
REVERT: D  140 PHE cc_start: 0.8217 (m-80) cc_final: 0.6312 (p90)
REVERT: D  143 ASP cc_start: 0.8329 (t0) cc_final: 0.8039 (m-30)
REVERT: D  145 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8207 (mt-10)
REVERT: D  146 ASP cc_start: 0.8447 (t0) cc_final: 0.8039 (t0)
REVERT: D  153 MET cc_start: 0.8648 (mmm) cc_final: 0.6739 (pp-130)
REVERT: D  155 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7197 (ptt90)
REVERT: D  163 ARG cc_start: 0.8865 (mtt180) cc_final: 0.7213 (pmt170)
REVERT: D  195 GLU cc_start: 0.5795 (tm-30) cc_final: 0.5575 (tm-30)
REVERT: D  207 ARG cc_start: 0.8348 (mtt180) cc_final: 0.6195 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8353 (mm-40)
REVERT: D  212 MET cc_start: 0.8770 (tpp) cc_final: 0.7103 (pmt)
REVERT: D  219 LYS cc_start: 0.8924 (ttmm) cc_final: 0.7902 (tptt)
REVERT: D  222 GLN cc_start: 0.8853 (mp-120) cc_final: 0.8399 (mp10)
REVERT: D  229 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7166 (pmt170)
  outliers start: 21
  outliers final: 8
  residues processed: 163
  average time/residue: 1.6387
  time to fit residues: 275.5559
Evaluate side-chains
  160 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.113699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.098021 restraints weight = 9822.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 2.93
r_work: 0.3974 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5710  Z= 0.270
  Angle     :  0.710   7.965   7720  Z= 0.380
  Chirality :  0.049   0.135    780
  Planarity :  0.003   0.022   1020
  Dihedral  :  5.554  21.436    780
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.67 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.75 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.020   0.003   PHE C 197 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.749 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.7855 (ttm) cc_final: 0.7432 (ttm)
REVERT: 1  153 MET cc_start: 0.7611 (mmm) cc_final: 0.7276 (mmm)
REVERT: 1  204 MET cc_start: 0.6041 (tmm) cc_final: 0.5625 (tmt)
REVERT: 1  205 MET cc_start: 0.8658 (ttm) cc_final: 0.8324 (mtm)
REVERT: A  133 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7208 (mtm)
REVERT: A  145 GLU cc_start: 0.8263 (mp0) cc_final: 0.7792 (mp0)
REVERT: A  155 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6739 (mpp80)
REVERT: A  195 GLU cc_start: 0.6371 (tm-30) cc_final: 0.6073 (tm-30)
REVERT: A  197 PHE cc_start: 0.6130 (m-10) cc_final: 0.5712 (m-10)
REVERT: A  211 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7417 (mt0)
REVERT: A  226 ASP cc_start: 0.7049 (p0) cc_final: 0.6767 (p0)
REVERT: B  100 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7576 (mttp)
REVERT: B  135 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.4817 (pmt170)
REVERT: B  140 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7171 (m-10)
REVERT: B  145 GLU cc_start: 0.8210 (mp0) cc_final: 0.7959 (mp0)
REVERT: B  149 TYR cc_start: 0.7372 (t80) cc_final: 0.6702 (t80)
REVERT: B  155 ARG cc_start: 0.7681 (mtt180) cc_final: 0.5986 (mmt-90)
REVERT: B  161 TYR cc_start: 0.8071 (m-10) cc_final: 0.7692 (m-10)
REVERT: B  175 VAL cc_start: 0.8617 (t) cc_final: 0.8181 (m)
REVERT: B  206 GLU cc_start: 0.8093 (tm-30) cc_final: 0.6873 (tm-30)
REVERT: B  207 ARG cc_start: 0.7695 (mtt180) cc_final: 0.5750 (tmm160)
REVERT: B  212 MET cc_start: 0.8263 (tpp) cc_final: 0.8010 (ttm)
REVERT: B  219 LYS cc_start: 0.7983 (mttt) cc_final: 0.6408 (pmtt)
REVERT: B  220 GLU cc_start: 0.8313 (mp0) cc_final: 0.7550 (pp20)
REVERT: B  228 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.5932 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7733 (m-40)
REVERT: C  137 MET cc_start: 0.7807 (ttm) cc_final: 0.7363 (ttm)
REVERT: C  147 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7711 (ptp-110)
REVERT: C  195 GLU cc_start: 0.4892 (tm-30) cc_final: 0.4268 (tt0)
REVERT: C  197 PHE cc_start: 0.5846 (m-10) cc_final: 0.5606 (m-10)
REVERT: C  204 MET cc_start: 0.6114 (tmt) cc_final: 0.5850 (tmt)
REVERT: C  220 GLU cc_start: 0.8652 (mp0) cc_final: 0.8055 (mp0)
REVERT: C  229 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6675 (mtp85)
REVERT: D  100 LYS cc_start: 0.7508 (mtmt) cc_final: 0.6474 (mmtt)
REVERT: D  133 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6459 (mpt)
REVERT: D  135 ARG cc_start: 0.7804 (mtt180) cc_final: 0.6979 (tpm170)
REVERT: D  140 PHE cc_start: 0.8423 (m-80) cc_final: 0.6226 (p90)
REVERT: D  143 ASP cc_start: 0.8148 (t0) cc_final: 0.7590 (m-30)
REVERT: D  145 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7799 (mt-10)
REVERT: D  146 ASP cc_start: 0.7966 (t0) cc_final: 0.7569 (t0)
REVERT: D  153 MET cc_start: 0.8586 (mmm) cc_final: 0.6510 (pp-130)
REVERT: D  155 ARG cc_start: 0.8218 (mtt180) cc_final: 0.6668 (ptt90)
REVERT: D  163 ARG cc_start: 0.8873 (mtt180) cc_final: 0.6940 (pmt170)
REVERT: D  207 ARG cc_start: 0.7965 (mtt180) cc_final: 0.5937 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7658 (mm-40)
REVERT: D  212 MET cc_start: 0.8853 (tpp) cc_final: 0.6955 (pmt)
REVERT: D  219 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7276 (tptt)
REVERT: D  222 GLN cc_start: 0.8286 (mp-120) cc_final: 0.7943 (mp10)
REVERT: D  229 ARG cc_start: 0.8212 (mtt180) cc_final: 0.6936 (pmt170)
  outliers start: 20
  outliers final: 6
  residues processed: 168
  average time/residue: 1.8795
  time to fit residues: 326.3896
Evaluate side-chains
  161 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0670
   chunk 42 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 51 optimal weight:    0.3980
   chunk 10 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.8522

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
A  96 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.114003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.098529 restraints weight = 9770.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 2.95
r_work: 0.3949 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5710  Z= 0.250
  Angle     :  0.731   8.163   7720  Z= 0.389
  Chirality :  0.049   0.138    780
  Planarity :  0.003   0.025   1020
  Dihedral  :  5.565  21.601    780
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.85 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.79 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.018   0.003   PHE C 197 
 TYR   0.028   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.600 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8018 (ttm) cc_final: 0.7586 (ttm)
REVERT: 1  153 MET cc_start: 0.7726 (mmm) cc_final: 0.7388 (mmm)
REVERT: 1  204 MET cc_start: 0.6138 (tmm) cc_final: 0.5658 (tmt)
REVERT: 1  205 MET cc_start: 0.8756 (ttm) cc_final: 0.8439 (mtm)
REVERT: 1  211 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8351 (mm-40)
REVERT: A  145 GLU cc_start: 0.8361 (mp0) cc_final: 0.7957 (mp0)
REVERT: A  155 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6878 (mpp80)
REVERT: A  193 LYS cc_start: 0.6382 (mmtt) cc_final: 0.6157 (mppt)
REVERT: A  195 GLU cc_start: 0.6407 (tm-30) cc_final: 0.6175 (tm-30)
REVERT: A  197 PHE cc_start: 0.6216 (m-10) cc_final: 0.5867 (m-10)
REVERT: A  211 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7438 (mt0)
REVERT: A  226 ASP cc_start: 0.7298 (p0) cc_final: 0.6896 (p0)
REVERT: B  100 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7613 (mttp)
REVERT: B  135 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5023 (pmt170)
REVERT: B  140 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7100 (m-10)
REVERT: B  145 GLU cc_start: 0.8255 (mp0) cc_final: 0.8018 (mp0)
REVERT: B  149 TYR cc_start: 0.7539 (t80) cc_final: 0.6870 (t80)
REVERT: B  155 ARG cc_start: 0.7804 (mtt180) cc_final: 0.6100 (mmt-90)
REVERT: B  161 TYR cc_start: 0.8200 (m-10) cc_final: 0.7829 (m-10)
REVERT: B  175 VAL cc_start: 0.8728 (t) cc_final: 0.8309 (m)
REVERT: B  206 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7764 (tm-30)
REVERT: B  212 MET cc_start: 0.8324 (tpp) cc_final: 0.8073 (ttm)
REVERT: B  219 LYS cc_start: 0.8071 (mttt) cc_final: 0.6472 (pmtt)
REVERT: B  220 GLU cc_start: 0.8212 (mp0) cc_final: 0.7561 (pp20)
REVERT: B  228 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.5969 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7868 (m-40)
REVERT: C  137 MET cc_start: 0.7984 (ttm) cc_final: 0.7537 (ttm)
REVERT: C  195 GLU cc_start: 0.4986 (tm-30) cc_final: 0.4088 (tt0)
REVERT: C  204 MET cc_start: 0.6179 (tmt) cc_final: 0.5861 (tmt)
REVERT: C  220 GLU cc_start: 0.8715 (mp0) cc_final: 0.8166 (mp0)
REVERT: C  229 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.6739 (mtp85)
REVERT: D  100 LYS cc_start: 0.7675 (mtmt) cc_final: 0.6664 (mmtt)
REVERT: D  133 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6662 (mpt)
REVERT: D  135 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7084 (tpm170)
REVERT: D  140 PHE cc_start: 0.8444 (m-80) cc_final: 0.6267 (p90)
REVERT: D  143 ASP cc_start: 0.8218 (t0) cc_final: 0.7672 (m-30)
REVERT: D  145 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7896 (mt-10)
REVERT: D  146 ASP cc_start: 0.8033 (t0) cc_final: 0.7658 (t0)
REVERT: D  153 MET cc_start: 0.8596 (mmm) cc_final: 0.6435 (pp-130)
REVERT: D  155 ARG cc_start: 0.8274 (mtt180) cc_final: 0.6748 (ptt90)
REVERT: D  163 ARG cc_start: 0.8920 (mtt180) cc_final: 0.6988 (pmt170)
REVERT: D  207 ARG cc_start: 0.8052 (mtt180) cc_final: 0.5965 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7787 (mm-40)
REVERT: D  212 MET cc_start: 0.8846 (tpp) cc_final: 0.6977 (pmt)
REVERT: D  219 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7355 (tptt)
REVERT: D  222 GLN cc_start: 0.8414 (mp-120) cc_final: 0.8042 (mp10)
REVERT: D  229 ARG cc_start: 0.8160 (mtt180) cc_final: 0.6930 (pmt170)
  outliers start: 17
  outliers final: 4
  residues processed: 161
  average time/residue: 1.4974
  time to fit residues: 249.2071
Evaluate side-chains
  162 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0980
   overall best weight:    2.6188

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.113368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.096828 restraints weight = 10038.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 2.98
r_work: 0.3869 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5710  Z= 0.302
  Angle     :  0.762   9.234   7720  Z= 0.406
  Chirality :  0.050   0.158    780
  Planarity :  0.003   0.026   1020
  Dihedral  :  5.673  21.765    780
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.19 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.83 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.054   0.004   PHE C 197 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.729 
Fit side-chains
REVERT: 1  137 MET cc_start: 0.8263 (ttm) cc_final: 0.7688 (ttm)
REVERT: 1  153 MET cc_start: 0.7867 (mmm) cc_final: 0.7581 (mmm)
REVERT: 1  204 MET cc_start: 0.6389 (tmm) cc_final: 0.6059 (tmt)
REVERT: 1  205 MET cc_start: 0.8943 (ttm) cc_final: 0.8735 (mtm)
REVERT: 1  211 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8679 (mm-40)
REVERT: A  145 GLU cc_start: 0.8492 (mp0) cc_final: 0.8141 (mp0)
REVERT: A  155 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7223 (mpp80)
REVERT: A  193 LYS cc_start: 0.6557 (mmtt) cc_final: 0.6321 (mppt)
REVERT: A  195 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6298 (tm-30)
REVERT: A  197 PHE cc_start: 0.7026 (m-10) cc_final: 0.6728 (m-10)
REVERT: A  211 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8459 (mp10)
REVERT: A  226 ASP cc_start: 0.7524 (p0) cc_final: 0.7147 (p0)
REVERT: B  100 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7756 (mttp)
REVERT: B  135 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.4993 (pmt170)
REVERT: B  140 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7147 (m-10)
REVERT: B  145 GLU cc_start: 0.8379 (mp0) cc_final: 0.8144 (mp0)
REVERT: B  149 TYR cc_start: 0.7830 (t80) cc_final: 0.7221 (t80)
REVERT: B  155 ARG cc_start: 0.8145 (mtt180) cc_final: 0.6445 (mmt-90)
REVERT: B  161 TYR cc_start: 0.8531 (m-10) cc_final: 0.8181 (m-10)
REVERT: B  175 VAL cc_start: 0.8937 (t) cc_final: 0.8543 (m)
REVERT: B  206 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7078 (tm-30)
REVERT: B  207 ARG cc_start: 0.7855 (mtt180) cc_final: 0.5901 (tmm160)
REVERT: B  212 MET cc_start: 0.8490 (tpp) cc_final: 0.8241 (ttm)
REVERT: B  219 LYS cc_start: 0.8159 (mttt) cc_final: 0.6564 (pmtt)
REVERT: B  220 GLU cc_start: 0.8332 (mp0) cc_final: 0.7597 (pp20)
REVERT: B  228 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.6051 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8119 (m-40)
REVERT: C  137 MET cc_start: 0.8233 (ttm) cc_final: 0.7811 (ttm)
REVERT: C  195 GLU cc_start: 0.5311 (tm-30) cc_final: 0.4627 (tt0)
REVERT: C  204 MET cc_start: 0.6505 (tmt) cc_final: 0.6163 (tmt)
REVERT: C  220 GLU cc_start: 0.8851 (mp0) cc_final: 0.8277 (mp0)
REVERT: C  229 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6897 (mtp85)
REVERT: D  100 LYS cc_start: 0.7832 (mtmt) cc_final: 0.6835 (mmtt)
REVERT: D  133 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6921 (mpt)
REVERT: D  135 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7217 (tpm170)
REVERT: D  140 PHE cc_start: 0.8411 (m-80) cc_final: 0.6283 (p90)
REVERT: D  143 ASP cc_start: 0.8333 (t0) cc_final: 0.7873 (m-30)
REVERT: D  145 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8080 (mt-10)
REVERT: D  146 ASP cc_start: 0.8282 (t0) cc_final: 0.7852 (t0)
REVERT: D  153 MET cc_start: 0.8600 (mmm) cc_final: 0.6503 (pp-130)
REVERT: D  155 ARG cc_start: 0.8417 (mtt180) cc_final: 0.6910 (ptt90)
REVERT: D  163 ARG cc_start: 0.8969 (mtt180) cc_final: 0.7090 (pmt170)
REVERT: D  207 ARG cc_start: 0.8215 (mtt180) cc_final: 0.6129 (mmp-170)
REVERT: D  212 MET cc_start: 0.8840 (tpp) cc_final: 0.7036 (pmt)
REVERT: D  219 LYS cc_start: 0.8660 (ttmm) cc_final: 0.7593 (tptt)
REVERT: D  222 GLN cc_start: 0.8657 (mp-120) cc_final: 0.8253 (mp10)
REVERT: D  229 ARG cc_start: 0.8142 (mtt180) cc_final: 0.6980 (pmt170)
  outliers start: 17
  outliers final: 5
  residues processed: 161
  average time/residue: 1.8593
  time to fit residues: 309.5761
Evaluate side-chains
  162 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 211 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.115439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.099092 restraints weight = 9960.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.95
r_work: 0.3888 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5710  Z= 0.242
  Angle     :  0.755   8.905   7720  Z= 0.402
  Chirality :  0.050   0.156    780
  Planarity :  0.003   0.028   1020
  Dihedral  :  5.629  21.759    780
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 23.03 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.87 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.043   0.004   PHE C 197 
 TYR   0.028   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5275.03 seconds
wall clock time: 92 minutes 9.17 seconds (5529.17 seconds total)