Starting phenix.real_space_refine
on Tue Feb 11 12:20:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7td6_25824/02_2025/7td6_25824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7td6_25824/02_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_25824/02_2025/7td6_25824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7td6_25824/02_2025/7td6_25824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7td6_25824/02_2025/7td6_25824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7td6_25824/02_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-5592/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: 5.15, per 1000 atoms: 0.92
  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: 1.23
  Conformation dependent library (CDL) restraints added in 653.4 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: 0.91
  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: 1.77

  Time building geometry restraints manager: 1.45 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: 0.05
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:             7.490
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     19.220
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:16.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.950
-------------------------------------------------------------------------------
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  : 0.877 
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: 1.6041
  time to fit residues: 331.2121
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  : 0.700 
-------------------------------------------------------------------------------
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 = 0.4287 r_free = 0.4287 target = 0.119119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.104253 restraints weight = 10029.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 2.87
r_work: 0.3977 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2450

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= 0.217
  Angle     :  0.596   6.466   7720  Z= 0.322
  Chirality :  0.047   0.131    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  4.599  16.757    780
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.62 %
    Favored  : 83.19 %
  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: -3.29 (0.26), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (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 1 110 
 PHE   0.015   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  : 0.574 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8514 (ptm-80) cc_final: 0.8273 (ptp90)
REVERT: 1  137 MET cc_start: 0.8457 (ttm) cc_final: 0.8199 (ttm)
REVERT: 1  153 MET cc_start: 0.7751 (mmm) cc_final: 0.7470 (mmm)
REVERT: 1  219 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7679 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8618 (mp0) cc_final: 0.8114 (mp0)
REVERT: 1  226 ASP cc_start: 0.7642 (m-30) cc_final: 0.7408 (t0)
REVERT: A  135 ARG cc_start: 0.8410 (ptp-110) cc_final: 0.8165 (ptp90)
REVERT: A  145 GLU cc_start: 0.8371 (mp0) cc_final: 0.8123 (mp0)
REVERT: A  193 LYS cc_start: 0.7071 (ttmm) cc_final: 0.6863 (mptt)
REVERT: A  197 PHE cc_start: 0.6774 (m-10) cc_final: 0.5778 (m-80)
REVERT: A  204 MET cc_start: 0.6683 (tmm) cc_final: 0.6372 (tmm)
REVERT: A  229 ARG cc_start: 0.8266 (mmt-90) cc_final: 0.7945 (mmt-90)
REVERT: B  135 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.4744 (pmt170)
REVERT: B  151 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7030 (pm20)
REVERT: B  155 ARG cc_start: 0.8439 (mtt180) cc_final: 0.6747 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8696 (t) cc_final: 0.8278 (m)
REVERT: B  212 MET cc_start: 0.8649 (tpp) cc_final: 0.8387 (ttm)
REVERT: B  219 LYS cc_start: 0.8175 (mttt) cc_final: 0.6585 (pmtt)
REVERT: B  220 GLU cc_start: 0.8305 (mp0) cc_final: 0.7548 (pp20)
REVERT: B  221 SER cc_start: 0.8911 (m) cc_final: 0.8451 (m)
REVERT: C  128 MET cc_start: 0.9122 (mtp) cc_final: 0.8872 (mtp)
REVERT: C  137 MET cc_start: 0.8375 (ttm) cc_final: 0.7972 (ttm)
REVERT: C  155 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7688 (mtp85)
REVERT: C  204 MET cc_start: 0.6767 (tmt) cc_final: 0.6321 (tmt)
REVERT: C  220 GLU cc_start: 0.8541 (mp0) cc_final: 0.8302 (mp0)
REVERT: D  100 LYS cc_start: 0.7452 (mtmt) cc_final: 0.6714 (mmtt)
REVERT: D  133 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6779 (mpt)
REVERT: D  135 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7321 (tpm170)
REVERT: D  140 PHE cc_start: 0.7976 (m-80) cc_final: 0.6707 (p90)
REVERT: D  143 ASP cc_start: 0.8387 (t0) cc_final: 0.7935 (m-30)
REVERT: D  153 MET cc_start: 0.8359 (mmm) cc_final: 0.6932 (ptt)
REVERT: D  155 ARG cc_start: 0.8267 (mtt180) cc_final: 0.6746 (ptt-90)
REVERT: D  163 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7267 (pmt170)
REVERT: D  177 ASP cc_start: 0.7875 (m-30) cc_final: 0.7478 (m-30)
REVERT: D  204 MET cc_start: 0.6888 (tmm) cc_final: 0.6608 (tmm)
REVERT: D  206 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7151 (tm-30)
REVERT: D  207 ARG cc_start: 0.7987 (mtt180) cc_final: 0.6502 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8205 (mm-40)
REVERT: D  212 MET cc_start: 0.8697 (tpp) cc_final: 0.6960 (pmt)
REVERT: D  222 GLN cc_start: 0.8672 (mp-120) cc_final: 0.8289 (mp10)
REVERT: D  224 TYR cc_start: 0.7963 (m-80) cc_final: 0.7542 (m-80)
REVERT: D  226 ASP cc_start: 0.7474 (p0) cc_final: 0.7050 (p0)
REVERT: D  229 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7142 (pmt170)
  outliers start: 13
  outliers final: 2
  residues processed: 168
  average time/residue: 1.4458
  time to fit residues: 251.5864
Evaluate side-chains
  163 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 158
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    4.1188

-------------------------------------------------------------------------------
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  96 ASN
A 172 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.112465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.096691 restraints weight = 10148.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.93
r_work: 0.3902 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   5710  Z= 0.410
  Angle     :  0.690   8.473   7720  Z= 0.374
  Chirality :  0.050   0.143    780
  Planarity :  0.003   0.021   1020
  Dihedral  :  5.528  20.107    780
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.31 %
    Favored  : 79.83 %
  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: -3.54 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.005   0.001   HIS 1 110 
 PHE   0.017   0.003   PHE B 174 
 TYR   0.028   0.003   TYR C 217 
 ARG   0.004   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
  179 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.716 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8417 (ptm-80) cc_final: 0.7975 (ptp90)
REVERT: 1  137 MET cc_start: 0.8116 (ttm) cc_final: 0.7627 (ttm)
REVERT: 1  153 MET cc_start: 0.7604 (mmm) cc_final: 0.7202 (mmm)
REVERT: 1  197 PHE cc_start: 0.6622 (m-10) cc_final: 0.5766 (m-10)
REVERT: 1  204 MET cc_start: 0.6203 (tmm) cc_final: 0.5937 (tmt)
REVERT: 1  205 MET cc_start: 0.8876 (ttm) cc_final: 0.8590 (mtt)
REVERT: 1  211 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8473 (mm-40)
REVERT: 1  220 GLU cc_start: 0.8596 (mp0) cc_final: 0.8182 (mp0)
REVERT: 1  224 TYR cc_start: 0.7814 (m-80) cc_final: 0.7506 (m-80)
REVERT: 1  226 ASP cc_start: 0.7740 (m-30) cc_final: 0.7458 (t0)
REVERT: A  145 GLU cc_start: 0.8395 (mp0) cc_final: 0.8068 (mp0)
REVERT: A  197 PHE cc_start: 0.6346 (m-10) cc_final: 0.4870 (m-10)
REVERT: A  211 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7714 (mt0)
REVERT: A  224 TYR cc_start: 0.7541 (m-80) cc_final: 0.7194 (m-80)
REVERT: A  226 ASP cc_start: 0.7440 (p0) cc_final: 0.6909 (p0)
REVERT: B  100 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7889 (mttp)
REVERT: B  140 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7596 (m-10)
REVERT: B  145 GLU cc_start: 0.8344 (mp0) cc_final: 0.8041 (mp0)
REVERT: B  155 ARG cc_start: 0.7975 (mtt180) cc_final: 0.6284 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8266 (tp30) cc_final: 0.7423 (tm-30)
REVERT: B  207 ARG cc_start: 0.7548 (mtt180) cc_final: 0.5808 (tmm160)
REVERT: B  212 MET cc_start: 0.8475 (tpp) cc_final: 0.8203 (ttm)
REVERT: B  219 LYS cc_start: 0.8124 (mttt) cc_final: 0.6634 (pmtt)
REVERT: B  220 GLU cc_start: 0.8326 (mp0) cc_final: 0.7522 (pp20)
REVERT: C  128 MET cc_start: 0.9106 (mtp) cc_final: 0.8799 (mtp)
REVERT: C  137 MET cc_start: 0.8030 (ttm) cc_final: 0.7566 (ttm)
REVERT: C  155 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7121 (mtt90)
REVERT: C  195 GLU cc_start: 0.5014 (tm-30) cc_final: 0.3926 (tt0)
REVERT: C  197 PHE cc_start: 0.6282 (m-10) cc_final: 0.5588 (m-10)
REVERT: C  204 MET cc_start: 0.6424 (tmt) cc_final: 0.6130 (tmt)
REVERT: C  220 GLU cc_start: 0.8695 (mp0) cc_final: 0.8192 (mp0)
REVERT: D  100 LYS cc_start: 0.7467 (mtmt) cc_final: 0.6641 (mmtt)
REVERT: D  135 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7121 (tpm170)
REVERT: D  140 PHE cc_start: 0.8218 (m-80) cc_final: 0.6289 (p90)
REVERT: D  143 ASP cc_start: 0.8221 (t0) cc_final: 0.7832 (m-30)
REVERT: D  146 ASP cc_start: 0.8043 (t0) cc_final: 0.7777 (t0)
REVERT: D  155 ARG cc_start: 0.8264 (mtt180) cc_final: 0.6643 (ptt90)
REVERT: D  158 ASN cc_start: 0.8691 (m110) cc_final: 0.8411 (m-40)
REVERT: D  163 ARG cc_start: 0.8642 (mtt180) cc_final: 0.6969 (pmt170)
REVERT: D  204 MET cc_start: 0.6545 (tmm) cc_final: 0.6193 (tmm)
REVERT: D  207 ARG cc_start: 0.7900 (mtt180) cc_final: 0.6025 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7877 (mm-40)
REVERT: D  212 MET cc_start: 0.8863 (tpp) cc_final: 0.6941 (pmt)
REVERT: D  221 SER cc_start: 0.8684 (p) cc_final: 0.8482 (m)
REVERT: D  222 GLN cc_start: 0.8317 (mp-120) cc_final: 0.7911 (mp10)
REVERT: D  224 TYR cc_start: 0.7784 (m-80) cc_final: 0.7348 (m-80)
REVERT: D  229 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7109 (pmt170)
  outliers start: 17
  outliers final: 5
  residues processed: 172
  average time/residue: 1.4956
  time to fit residues: 266.0933
Evaluate side-chains
  159 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
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:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 173 ASN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.111908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.096378 restraints weight = 10184.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.95
r_work: 0.3906 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5710  Z= 0.328
  Angle     :  0.653   7.539   7720  Z= 0.353
  Chirality :  0.049   0.138    780
  Planarity :  0.003   0.018   1020
  Dihedral  :  5.593  20.350    780
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 18.32 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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   0.011   0.001   TRP A  98 
 HIS   0.005   0.001   HIS 1 110 
 PHE   0.015   0.003   PHE B 174 
 TYR   0.029   0.002   TYR 1 217 
 ARG   0.003   0.000   ARG B 135 

*********************** 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
  177 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.620 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7957 (ptp90)
REVERT: 1  137 MET cc_start: 0.8068 (ttm) cc_final: 0.7720 (ttm)
REVERT: 1  153 MET cc_start: 0.7637 (mmm) cc_final: 0.7236 (mmm)
REVERT: 1  197 PHE cc_start: 0.6179 (m-10) cc_final: 0.5877 (m-10)
REVERT: 1  204 MET cc_start: 0.6107 (tmm) cc_final: 0.5829 (tmt)
REVERT: 1  205 MET cc_start: 0.8822 (ttm) cc_final: 0.8389 (mtm)
REVERT: A  135 ARG cc_start: 0.8420 (ptp90) cc_final: 0.8194 (ptp90)
REVERT: A  145 GLU cc_start: 0.8355 (mp0) cc_final: 0.7924 (mp0)
REVERT: A  155 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7110 (mpt-90)
REVERT: A  197 PHE cc_start: 0.6325 (m-10) cc_final: 0.5089 (m-10)
REVERT: A  210 GLU cc_start: 0.7758 (mp0) cc_final: 0.7233 (mp0)
REVERT: A  211 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7895 (mt0)
REVERT: A  226 ASP cc_start: 0.7358 (p0) cc_final: 0.7100 (p0)
REVERT: B  100 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7617 (mttp)
REVERT: B  135 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.4786 (pmt170)
REVERT: B  145 GLU cc_start: 0.8312 (mp0) cc_final: 0.8022 (mp0)
REVERT: B  146 ASP cc_start: 0.8191 (t0) cc_final: 0.7971 (t0)
REVERT: B  155 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6215 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8183 (tp30) cc_final: 0.7302 (tm-30)
REVERT: B  207 ARG cc_start: 0.7530 (mtt180) cc_final: 0.5799 (tmm160)
REVERT: B  212 MET cc_start: 0.8451 (tpp) cc_final: 0.8167 (ttm)
REVERT: B  219 LYS cc_start: 0.8091 (mttt) cc_final: 0.6483 (pmtt)
REVERT: B  220 GLU cc_start: 0.8232 (mp0) cc_final: 0.7535 (pp20)
REVERT: C  128 MET cc_start: 0.9034 (mtp) cc_final: 0.8734 (mtp)
REVERT: C  137 MET cc_start: 0.7953 (ttm) cc_final: 0.7505 (ttm)
REVERT: C  155 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7474 (mtt180)
REVERT: C  195 GLU cc_start: 0.4971 (tm-30) cc_final: 0.4004 (tt0)
REVERT: C  197 PHE cc_start: 0.6271 (m-10) cc_final: 0.5950 (m-10)
REVERT: C  204 MET cc_start: 0.6317 (tmt) cc_final: 0.5991 (tmt)
REVERT: C  210 GLU cc_start: 0.7453 (mp0) cc_final: 0.6919 (tm-30)
REVERT: C  220 GLU cc_start: 0.8747 (mp0) cc_final: 0.8138 (mp0)
REVERT: D  100 LYS cc_start: 0.7623 (mtmt) cc_final: 0.6691 (mmtt)
REVERT: D  133 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6292 (mpt)
REVERT: D  135 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7181 (tpm170)
REVERT: D  140 PHE cc_start: 0.8318 (m-80) cc_final: 0.6344 (p90)
REVERT: D  143 ASP cc_start: 0.8179 (t0) cc_final: 0.7753 (m-30)
REVERT: D  145 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7864 (mt-10)
REVERT: D  146 ASP cc_start: 0.8085 (t0) cc_final: 0.7757 (t0)
REVERT: D  148 TYR cc_start: 0.8157 (p90) cc_final: 0.7802 (p90)
REVERT: D  153 MET cc_start: 0.8537 (mmm) cc_final: 0.6531 (pp-130)
REVERT: D  155 ARG cc_start: 0.8213 (mtt180) cc_final: 0.6614 (ptt90)
REVERT: D  158 ASN cc_start: 0.8640 (m110) cc_final: 0.8349 (m-40)
REVERT: D  163 ARG cc_start: 0.8776 (mtt180) cc_final: 0.6964 (pmt170)
REVERT: D  204 MET cc_start: 0.6508 (tmm) cc_final: 0.6181 (tmm)
REVERT: D  207 ARG cc_start: 0.7967 (mtt180) cc_final: 0.5894 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7748 (mm-40)
REVERT: D  212 MET cc_start: 0.8894 (tpp) cc_final: 0.6977 (pmt)
REVERT: D  221 SER cc_start: 0.8689 (p) cc_final: 0.8459 (m)
REVERT: D  222 GLN cc_start: 0.8232 (mp-120) cc_final: 0.7873 (mp10)
REVERT: D  224 TYR cc_start: 0.7670 (m-80) cc_final: 0.7247 (m-80)
REVERT: D  229 ARG cc_start: 0.8306 (mtt180) cc_final: 0.7059 (pmt170)
  outliers start: 23
  outliers final: 5
  residues processed: 166
  average time/residue: 1.5769
  time to fit residues: 270.4586
Evaluate side-chains
  160 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
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  155 ARG
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  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0980
   chunk 50 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    1.6188

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
B 142 ASN
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** 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 = 0.4203 r_free = 0.4203 target = 0.114553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.098887 restraints weight = 9816.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 2.95
r_work: 0.3890 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5710  Z= 0.204
  Angle     :  0.624   7.802   7720  Z= 0.335
  Chirality :  0.048   0.133    780
  Planarity :  0.002   0.020   1020
  Dihedral  :  5.408  20.484    780
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.17 %
    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: -3.68 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.030   0.002   PHE B 197 
 TYR   0.028   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
  179 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.597 
Fit side-chains
REVERT: 1   96 ASN cc_start: 0.7949 (t0) cc_final: 0.7606 (t0)
REVERT: 1  135 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.8059 (ptp90)
REVERT: 1  137 MET cc_start: 0.8243 (ttm) cc_final: 0.7712 (ttm)
REVERT: 1  153 MET cc_start: 0.7801 (mmm) cc_final: 0.7446 (mmm)
REVERT: 1  197 PHE cc_start: 0.6375 (m-10) cc_final: 0.6165 (m-10)
REVERT: 1  204 MET cc_start: 0.6313 (tmm) cc_final: 0.5825 (tmt)
REVERT: A  145 GLU cc_start: 0.8470 (mp0) cc_final: 0.8034 (mp0)
REVERT: A  210 GLU cc_start: 0.7882 (mp0) cc_final: 0.7402 (mp0)
REVERT: A  211 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8010 (mt0)
REVERT: B  100 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7767 (mttp)
REVERT: B  145 GLU cc_start: 0.8363 (mp0) cc_final: 0.8100 (mp0)
REVERT: B  146 ASP cc_start: 0.8358 (t0) cc_final: 0.8071 (t0)
REVERT: B  155 ARG cc_start: 0.8021 (mtt180) cc_final: 0.6368 (mmp-170)
REVERT: B  204 MET cc_start: 0.7324 (tmm) cc_final: 0.7113 (tmm)
REVERT: B  206 GLU cc_start: 0.8169 (tp30) cc_final: 0.7696 (tm-30)
REVERT: B  207 ARG cc_start: 0.7603 (mtt180) cc_final: 0.5808 (tmm160)
REVERT: B  212 MET cc_start: 0.8471 (tpp) cc_final: 0.8233 (ttm)
REVERT: B  219 LYS cc_start: 0.8129 (mttt) cc_final: 0.6506 (pmtt)
REVERT: B  220 GLU cc_start: 0.8196 (mp0) cc_final: 0.7579 (pp20)
REVERT: C  128 MET cc_start: 0.9122 (mtp) cc_final: 0.8849 (mtp)
REVERT: C  137 MET cc_start: 0.8144 (ttm) cc_final: 0.7703 (ttm)
REVERT: C  195 GLU cc_start: 0.5060 (tm-30) cc_final: 0.4125 (tt0)
REVERT: C  204 MET cc_start: 0.6439 (tmt) cc_final: 0.6124 (tmt)
REVERT: C  210 GLU cc_start: 0.7401 (mp0) cc_final: 0.7137 (tm-30)
REVERT: C  211 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7768 (mt0)
REVERT: C  220 GLU cc_start: 0.8813 (mp0) cc_final: 0.8217 (mp0)
REVERT: D  100 LYS cc_start: 0.7648 (mtmt) cc_final: 0.6695 (mmtt)
REVERT: D  135 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7340 (tpm170)
REVERT: D  140 PHE cc_start: 0.8298 (m-80) cc_final: 0.6230 (p90)
REVERT: D  143 ASP cc_start: 0.8242 (t0) cc_final: 0.7798 (m-30)
REVERT: D  145 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7929 (mt-10)
REVERT: D  146 ASP cc_start: 0.8233 (t0) cc_final: 0.7868 (t0)
REVERT: D  148 TYR cc_start: 0.8208 (p90) cc_final: 0.7940 (p90)
REVERT: D  153 MET cc_start: 0.8592 (mmm) cc_final: 0.6578 (pp-130)
REVERT: D  155 ARG cc_start: 0.8276 (mtt180) cc_final: 0.6826 (ptt90)
REVERT: D  158 ASN cc_start: 0.8730 (m110) cc_final: 0.8458 (m-40)
REVERT: D  163 ARG cc_start: 0.8829 (mtt180) cc_final: 0.7051 (pmt170)
REVERT: D  204 MET cc_start: 0.6637 (tmm) cc_final: 0.6262 (tmm)
REVERT: D  207 ARG cc_start: 0.8164 (mtt180) cc_final: 0.5974 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7781 (mm-40)
REVERT: D  212 MET cc_start: 0.8865 (tpp) cc_final: 0.6999 (pmt)
REVERT: D  219 LYS cc_start: 0.8692 (ttmm) cc_final: 0.7416 (tptt)
REVERT: D  222 GLN cc_start: 0.8429 (mp-120) cc_final: 0.8016 (mp10)
REVERT: D  224 TYR cc_start: 0.7829 (m-80) cc_final: 0.7440 (m-80)
REVERT: D  229 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7086 (pmt170)
  outliers start: 19
  outliers final: 5
  residues processed: 169
  average time/residue: 1.5818
  time to fit residues: 275.8486
Evaluate side-chains
  157 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  211 GLN
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    3.0588

-------------------------------------------------------------------------------
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 173 ASN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.112406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.096732 restraints weight = 9891.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 2.94
r_work: 0.3957 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
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      :  0.005   0.034   5710  Z= 0.319
  Angle     :  0.675   7.912   7720  Z= 0.363
  Chirality :  0.049   0.157    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  5.602  21.886    780
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.50 %
    Favored  : 77.48 %
  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   0.007   0.001   TRP A  98 
 HIS   0.005   0.001   HIS 1 110 
 PHE   0.017   0.003   PHE C 197 
 TYR   0.031   0.002   TYR C 217 
 ARG   0.004   0.000   ARG B 135 

*********************** 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
  173 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.675 
Fit side-chains
REVERT: 1   96 ASN cc_start: 0.7529 (t0) cc_final: 0.7242 (t0)
REVERT: 1  135 ARG cc_start: 0.8323 (ptm-80) cc_final: 0.7931 (ptp90)
REVERT: 1  137 MET cc_start: 0.7992 (ttm) cc_final: 0.7614 (ttm)
REVERT: 1  146 ASP cc_start: 0.7873 (t0) cc_final: 0.7635 (t0)
REVERT: 1  153 MET cc_start: 0.7611 (mmm) cc_final: 0.7281 (mmm)
REVERT: 1  197 PHE cc_start: 0.6152 (m-10) cc_final: 0.5907 (m-10)
REVERT: 1  204 MET cc_start: 0.6061 (tmm) cc_final: 0.5745 (tmt)
REVERT: 1  205 MET cc_start: 0.8751 (ttm) cc_final: 0.8454 (mtm)
REVERT: 1  211 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8332 (mm-40)
REVERT: 1  226 ASP cc_start: 0.7830 (m-30) cc_final: 0.7588 (m-30)
REVERT: A  133 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7209 (mtm)
REVERT: A  145 GLU cc_start: 0.8322 (mp0) cc_final: 0.7808 (mp0)
REVERT: A  197 PHE cc_start: 0.6145 (m-10) cc_final: 0.5028 (m-10)
REVERT: A  211 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7639 (mt0)
REVERT: B  100 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7662 (mttp)
REVERT: B  135 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.4869 (pmt170)
REVERT: B  145 GLU cc_start: 0.8324 (mp0) cc_final: 0.7966 (mp0)
REVERT: B  146 ASP cc_start: 0.8189 (t0) cc_final: 0.7793 (t0)
REVERT: B  155 ARG cc_start: 0.7710 (mtt180) cc_final: 0.5996 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8129 (tp30) cc_final: 0.7722 (tm-30)
REVERT: B  207 ARG cc_start: 0.7426 (mtt180) cc_final: 0.5691 (tmm160)
REVERT: B  212 MET cc_start: 0.8308 (tpp) cc_final: 0.8031 (ttm)
REVERT: B  219 LYS cc_start: 0.8042 (mttt) cc_final: 0.6482 (pmtt)
REVERT: B  220 GLU cc_start: 0.8285 (mp0) cc_final: 0.7552 (pp20)
REVERT: B  229 ARG cc_start: 0.3468 (mmp-170) cc_final: 0.3125 (mmp-170)
REVERT: C  107 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7749 (m-40)
REVERT: C  128 MET cc_start: 0.9005 (mtp) cc_final: 0.8731 (mtp)
REVERT: C  137 MET cc_start: 0.7859 (ttm) cc_final: 0.7411 (ttm)
REVERT: C  197 PHE cc_start: 0.5820 (m-10) cc_final: 0.4952 (m-10)
REVERT: C  204 MET cc_start: 0.6232 (tmt) cc_final: 0.5966 (tmt)
REVERT: C  220 GLU cc_start: 0.8672 (mp0) cc_final: 0.8075 (mp0)
REVERT: D  100 LYS cc_start: 0.7536 (mtmt) cc_final: 0.6543 (mmtt)
REVERT: D  133 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6452 (mpt)
REVERT: D  135 ARG cc_start: 0.7823 (mtt180) cc_final: 0.6990 (tpm170)
REVERT: D  140 PHE cc_start: 0.8345 (m-80) cc_final: 0.6165 (p90)
REVERT: D  143 ASP cc_start: 0.8159 (t0) cc_final: 0.7681 (m-30)
REVERT: D  145 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7944 (mt-10)
REVERT: D  146 ASP cc_start: 0.8035 (t0) cc_final: 0.7635 (t0)
REVERT: D  153 MET cc_start: 0.8592 (mmm) cc_final: 0.6524 (pp-130)
REVERT: D  155 ARG cc_start: 0.8198 (mtt180) cc_final: 0.6668 (ptt90)
REVERT: D  158 ASN cc_start: 0.8598 (m110) cc_final: 0.8300 (m-40)
REVERT: D  163 ARG cc_start: 0.8836 (mtt180) cc_final: 0.6928 (pmt170)
REVERT: D  204 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5947 (tmm)
REVERT: D  207 ARG cc_start: 0.7990 (mtt180) cc_final: 0.5810 (mmp-170)
REVERT: D  211 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7627 (mm-40)
REVERT: D  212 MET cc_start: 0.8882 (tpp) cc_final: 0.6981 (pmt)
REVERT: D  219 LYS cc_start: 0.8316 (ttmm) cc_final: 0.7259 (tptt)
REVERT: D  222 GLN cc_start: 0.8194 (mp-120) cc_final: 0.7870 (mp10)
REVERT: D  224 TYR cc_start: 0.7631 (m-80) cc_final: 0.7211 (m-80)
REVERT: D  229 ARG cc_start: 0.8237 (mtt180) cc_final: 0.6955 (pmt170)
  outliers start: 18
  outliers final: 5
  residues processed: 163
  average time/residue: 1.5707
  time to fit residues: 264.8135
Evaluate side-chains
  164 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  204 MET
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:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** 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 = 0.4153 r_free = 0.4153 target = 0.112675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.096422 restraints weight = 10057.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.96
r_work: 0.3838 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5710  Z= 0.324
  Angle     :  0.687   8.103   7720  Z= 0.369
  Chirality :  0.049   0.145    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  5.637  23.146    780
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.17 %
    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: -3.78 (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   0.007   0.001   TRP B  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.024   0.003   PHE B 197 
 TYR   0.031   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
  169 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.689 
Fit side-chains
REVERT: 1   96 ASN cc_start: 0.7873 (t0) cc_final: 0.7639 (t0)
REVERT: 1  135 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.8100 (ptp90)
REVERT: 1  137 MET cc_start: 0.8225 (ttm) cc_final: 0.7884 (ttm)
REVERT: 1  153 MET cc_start: 0.7839 (mmm) cc_final: 0.7531 (mmm)
REVERT: 1  197 PHE cc_start: 0.6291 (m-10) cc_final: 0.5991 (m-10)
REVERT: 1  204 MET cc_start: 0.6381 (tmm) cc_final: 0.6095 (tmt)
REVERT: 1  205 MET cc_start: 0.8913 (ttm) cc_final: 0.8463 (mtt)
REVERT: A  133 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7449 (mtm)
REVERT: A  145 GLU cc_start: 0.8480 (mp0) cc_final: 0.7979 (mp0)
REVERT: A  197 PHE cc_start: 0.6333 (m-10) cc_final: 0.5251 (m-10)
REVERT: A  210 GLU cc_start: 0.7912 (mp0) cc_final: 0.7665 (mp0)
REVERT: A  226 ASP cc_start: 0.7471 (p0) cc_final: 0.7209 (p0)
REVERT: B  100 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7750 (mttp)
REVERT: B  135 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5046 (pmt170)
REVERT: B  145 GLU cc_start: 0.8430 (mp0) cc_final: 0.8153 (mp0)
REVERT: B  146 ASP cc_start: 0.8373 (t0) cc_final: 0.8020 (t0)
REVERT: B  155 ARG cc_start: 0.8092 (mtt180) cc_final: 0.6327 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8140 (tp30) cc_final: 0.7767 (tm-30)
REVERT: B  207 ARG cc_start: 0.7576 (mtt180) cc_final: 0.5787 (tmm160)
REVERT: B  212 MET cc_start: 0.8504 (tpp) cc_final: 0.8236 (ttm)
REVERT: B  219 LYS cc_start: 0.8175 (mttt) cc_final: 0.6585 (pmtt)
REVERT: B  220 GLU cc_start: 0.8328 (mp0) cc_final: 0.7575 (pp20)
REVERT: C  107 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8020 (m-40)
REVERT: C  128 MET cc_start: 0.9142 (mtp) cc_final: 0.8928 (mtp)
REVERT: C  137 MET cc_start: 0.8133 (ttm) cc_final: 0.7672 (ttm)
REVERT: C  195 GLU cc_start: 0.5146 (tm-30) cc_final: 0.3953 (tt0)
REVERT: C  204 MET cc_start: 0.6493 (tmt) cc_final: 0.6165 (tmt)
REVERT: C  210 GLU cc_start: 0.7399 (mp0) cc_final: 0.7093 (tm-30)
REVERT: C  211 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8027 (mt0)
REVERT: C  220 GLU cc_start: 0.8802 (mp0) cc_final: 0.8212 (mp0)
REVERT: C  229 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6892 (mtp85)
REVERT: D  100 LYS cc_start: 0.7795 (mtmt) cc_final: 0.6773 (mmtt)
REVERT: D  133 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6748 (mpt)
REVERT: D  135 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7205 (tpm170)
REVERT: D  140 PHE cc_start: 0.8379 (m-80) cc_final: 0.6229 (p90)
REVERT: D  143 ASP cc_start: 0.8350 (t0) cc_final: 0.7811 (m-30)
REVERT: D  145 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8176 (mt-10)
REVERT: D  146 ASP cc_start: 0.8290 (t0) cc_final: 0.7832 (t0)
REVERT: D  153 MET cc_start: 0.8624 (mmm) cc_final: 0.6580 (pp-130)
REVERT: D  155 ARG cc_start: 0.8337 (mtt180) cc_final: 0.6779 (ptt90)
REVERT: D  158 ASN cc_start: 0.8747 (m110) cc_final: 0.8470 (m-40)
REVERT: D  163 ARG cc_start: 0.8914 (mtt180) cc_final: 0.6989 (pmt170)
REVERT: D  204 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6343 (tmm)
REVERT: D  207 ARG cc_start: 0.8121 (mtt180) cc_final: 0.5956 (mmp-170)
REVERT: D  212 MET cc_start: 0.8864 (tpp) cc_final: 0.7042 (pmt)
REVERT: D  219 LYS cc_start: 0.8583 (ttmm) cc_final: 0.7383 (tptt)
REVERT: D  222 GLN cc_start: 0.8458 (mp-120) cc_final: 0.8068 (mp10)
REVERT: D  229 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7039 (pmt170)
  outliers start: 19
  outliers final: 6
  residues processed: 158
  average time/residue: 1.5817
  time to fit residues: 258.2858
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  : 0.706 
-------------------------------------------------------------------------------
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  133 MET
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  190 THR
Chi-restraints excluded: chain C residue  211 GLN
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  204 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0770
   overall best weight:    2.5944

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.112167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.095794 restraints weight = 10052.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.97
r_work: 0.3840 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.4164

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= 0.292
  Angle     :  0.700   8.223   7720  Z= 0.374
  Chirality :  0.049   0.143    780
  Planarity :  0.003   0.022   1020
  Dihedral  :  5.618  23.611    780
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.00 %
    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: -3.80 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.017   0.003   PHE C 197 
 TYR   0.032   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
  169 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.645 
Fit side-chains
REVERT: 1   96 ASN cc_start: 0.7809 (t0) cc_final: 0.7587 (t0)
REVERT: 1  135 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.8026 (ptp90)
REVERT: 1  137 MET cc_start: 0.8159 (ttm) cc_final: 0.7786 (ttm)
REVERT: 1  146 ASP cc_start: 0.8053 (t0) cc_final: 0.7849 (t0)
REVERT: 1  153 MET cc_start: 0.7805 (mmm) cc_final: 0.7491 (mmm)
REVERT: 1  197 PHE cc_start: 0.6272 (m-10) cc_final: 0.5979 (m-10)
REVERT: 1  204 MET cc_start: 0.6403 (tmm) cc_final: 0.6144 (tmt)
REVERT: 1  205 MET cc_start: 0.8905 (ttm) cc_final: 0.8487 (mtt)
REVERT: A  133 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7380 (mtm)
REVERT: A  145 GLU cc_start: 0.8463 (mp0) cc_final: 0.7959 (mp0)
REVERT: A  197 PHE cc_start: 0.6422 (m-10) cc_final: 0.5367 (m-10)
REVERT: B  100 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7742 (mttp)
REVERT: B  145 GLU cc_start: 0.8404 (mp0) cc_final: 0.8108 (mp0)
REVERT: B  146 ASP cc_start: 0.8384 (t0) cc_final: 0.7969 (t0)
REVERT: B  155 ARG cc_start: 0.8036 (mtt180) cc_final: 0.6275 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8242 (tp30) cc_final: 0.7771 (tm-30)
REVERT: B  207 ARG cc_start: 0.7568 (mtt180) cc_final: 0.5766 (tmm160)
REVERT: B  212 MET cc_start: 0.8432 (tpp) cc_final: 0.8169 (ttm)
REVERT: B  219 LYS cc_start: 0.8148 (mttt) cc_final: 0.6551 (pmtt)
REVERT: B  220 GLU cc_start: 0.8335 (mp0) cc_final: 0.7613 (pp20)
REVERT: C  107 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7973 (m-40)
REVERT: C  128 MET cc_start: 0.9126 (mtp) cc_final: 0.8846 (mtp)
REVERT: C  137 MET cc_start: 0.8051 (ttm) cc_final: 0.7588 (ttm)
REVERT: C  195 GLU cc_start: 0.5216 (tm-30) cc_final: 0.4200 (tt0)
REVERT: C  204 MET cc_start: 0.6450 (tmt) cc_final: 0.6133 (tmt)
REVERT: C  220 GLU cc_start: 0.8779 (mp0) cc_final: 0.8175 (mp0)
REVERT: C  229 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6801 (mtp85)
REVERT: D  100 LYS cc_start: 0.7769 (mtmt) cc_final: 0.6756 (mmtt)
REVERT: D  133 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6688 (mpt)
REVERT: D  135 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7175 (tpm170)
REVERT: D  140 PHE cc_start: 0.8435 (m-80) cc_final: 0.6213 (p90)
REVERT: D  143 ASP cc_start: 0.8345 (t0) cc_final: 0.7829 (m-30)
REVERT: D  145 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8122 (mt-10)
REVERT: D  146 ASP cc_start: 0.8230 (t0) cc_final: 0.7811 (t0)
REVERT: D  153 MET cc_start: 0.8624 (mmm) cc_final: 0.6569 (pp-130)
REVERT: D  155 ARG cc_start: 0.8321 (mtt180) cc_final: 0.6768 (ptt90)
REVERT: D  163 ARG cc_start: 0.8973 (mtt180) cc_final: 0.6994 (pmt170)
REVERT: D  204 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6235 (tmm)
REVERT: D  207 ARG cc_start: 0.8133 (mtt180) cc_final: 0.5947 (mmp-170)
REVERT: D  212 MET cc_start: 0.8893 (tpp) cc_final: 0.6973 (pmt)
REVERT: D  219 LYS cc_start: 0.8535 (ttmm) cc_final: 0.7355 (tptt)
REVERT: D  229 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7021 (pmt170)
  outliers start: 20
  outliers final: 8
  residues processed: 158
  average time/residue: 1.5897
  time to fit residues: 259.3750
Evaluate side-chains
  161 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
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  133 MET
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A 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  204 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** 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 = 0.4175 r_free = 0.4175 target = 0.113885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.097334 restraints weight = 10016.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 3.01
r_work: 0.3915 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.4139

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= 0.236
  Angle     :  0.707   8.205   7720  Z= 0.378
  Chirality :  0.050   0.196    780
  Planarity :  0.003   0.025   1020
  Dihedral  :  5.539  23.750    780
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.67 %
    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: -3.81 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.021   0.002   PHE B 197 
 TYR   0.032   0.002   TYR C 217 
 ARG   0.009   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
  173 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.673 
Fit side-chains
REVERT: 1   96 ASN cc_start: 0.7661 (t0) cc_final: 0.7438 (t0)
REVERT: 1  135 ARG cc_start: 0.8412 (ptm-80) cc_final: 0.7921 (ptp90)
REVERT: 1  137 MET cc_start: 0.7989 (ttm) cc_final: 0.7609 (ttm)
REVERT: 1  153 MET cc_start: 0.7676 (mmm) cc_final: 0.7364 (mmm)
REVERT: 1  197 PHE cc_start: 0.6186 (m-10) cc_final: 0.5822 (m-10)
REVERT: 1  204 MET cc_start: 0.6228 (tmm) cc_final: 0.5753 (tmt)
REVERT: 1  205 MET cc_start: 0.8962 (ttm) cc_final: 0.8685 (mtp)
REVERT: 1  211 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8320 (mm-40)
REVERT: A  133 MET cc_start: 0.7509 (mpt) cc_final: 0.7169 (mtm)
REVERT: A  145 GLU cc_start: 0.8381 (mp0) cc_final: 0.7893 (mp0)
REVERT: A  193 LYS cc_start: 0.6354 (mmtt) cc_final: 0.5938 (mppt)
REVERT: A  195 GLU cc_start: 0.6047 (tm-30) cc_final: 0.5333 (tm-30)
REVERT: A  197 PHE cc_start: 0.6292 (m-10) cc_final: 0.5361 (m-10)
REVERT: A  211 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7369 (mt0)
REVERT: B  100 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7625 (mttp)
REVERT: B  145 GLU cc_start: 0.8343 (mp0) cc_final: 0.8038 (mp0)
REVERT: B  146 ASP cc_start: 0.8189 (t0) cc_final: 0.7803 (t0)
REVERT: B  155 ARG cc_start: 0.7835 (mtt180) cc_final: 0.6093 (mmp-170)
REVERT: B  206 GLU cc_start: 0.7701 (tp30) cc_final: 0.7490 (tm-30)
REVERT: B  207 ARG cc_start: 0.7441 (mtt180) cc_final: 0.5576 (tmm160)
REVERT: B  212 MET cc_start: 0.8293 (tpp) cc_final: 0.8014 (ttm)
REVERT: B  219 LYS cc_start: 0.8034 (mttt) cc_final: 0.6462 (pmtt)
REVERT: B  220 GLU cc_start: 0.8273 (mp0) cc_final: 0.7572 (pp20)
REVERT: C  107 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7801 (m-40)
REVERT: C  128 MET cc_start: 0.9045 (mtp) cc_final: 0.8790 (mtp)
REVERT: C  137 MET cc_start: 0.7852 (ttm) cc_final: 0.7444 (ttm)
REVERT: C  147 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7741 (ptp-110)
REVERT: C  195 GLU cc_start: 0.5037 (tm-30) cc_final: 0.4205 (tt0)
REVERT: C  197 PHE cc_start: 0.5990 (m-10) cc_final: 0.5226 (m-10)
REVERT: C  204 MET cc_start: 0.6305 (tmt) cc_final: 0.5986 (tmt)
REVERT: C  211 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8137 (mm-40)
REVERT: C  220 GLU cc_start: 0.8717 (mp0) cc_final: 0.8100 (mp0)
REVERT: C  229 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6713 (mtp85)
REVERT: D  100 LYS cc_start: 0.7617 (mtmt) cc_final: 0.6606 (mmtt)
REVERT: D  133 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6582 (mpt)
REVERT: D  135 ARG cc_start: 0.7848 (mtt180) cc_final: 0.6957 (tpm170)
REVERT: D  140 PHE cc_start: 0.8413 (m-80) cc_final: 0.6131 (p90)
REVERT: D  143 ASP cc_start: 0.8240 (t0) cc_final: 0.7596 (m-30)
REVERT: D  145 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7922 (mt-10)
REVERT: D  146 ASP cc_start: 0.8014 (t0) cc_final: 0.7630 (t0)
REVERT: D  152 ASN cc_start: 0.8517 (m-40) cc_final: 0.7807 (m110)
REVERT: D  153 MET cc_start: 0.8570 (mmm) cc_final: 0.6423 (pp-130)
REVERT: D  155 ARG cc_start: 0.8234 (mtt180) cc_final: 0.6658 (ptt90)
REVERT: D  158 ASN cc_start: 0.8609 (m110) cc_final: 0.8264 (m-40)
REVERT: D  163 ARG cc_start: 0.8936 (mtt180) cc_final: 0.6949 (pmt170)
REVERT: D  177 ASP cc_start: 0.7955 (m-30) cc_final: 0.7599 (m-30)
REVERT: D  207 ARG cc_start: 0.8051 (mtt180) cc_final: 0.5789 (mmp-170)
REVERT: D  212 MET cc_start: 0.8841 (tpp) cc_final: 0.6939 (pmt)
REVERT: D  219 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7196 (tptt)
REVERT: D  229 ARG cc_start: 0.8158 (mtt180) cc_final: 0.6891 (pmt170)
  outliers start: 19
  outliers final: 8
  residues processed: 164
  average time/residue: 1.6049
  time to fit residues: 271.6566
Evaluate side-chains
  161 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  137 MET
Chi-restraints excluded: chain A residue  211 GLN
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  211 GLN
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  107 ASN
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 25 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** 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 = 0.4150 r_free = 0.4150 target = 0.111945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.095779 restraints weight = 10136.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.92
r_work: 0.3853 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   5710  Z= 0.399
  Angle     :  0.800   8.672   7720  Z= 0.427
  Chirality :  0.051   0.203    780
  Planarity :  0.003   0.025   1020
  Dihedral  :  5.784  24.125    780
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 22.86 %
    Favored  : 74.79 %
  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: -3.84 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  98 
 HIS   0.005   0.001   HIS 1 110 
 PHE   0.015   0.003   PHE 1 174 
 TYR   0.030   0.003   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
  159 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.700 
Fit side-chains
REVERT: 1   96 ASN cc_start: 0.7748 (t0) cc_final: 0.7539 (t0)
REVERT: 1  135 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.8042 (ptp90)
REVERT: 1  137 MET cc_start: 0.8063 (ttm) cc_final: 0.7719 (ttm)
REVERT: 1  153 MET cc_start: 0.7824 (mmm) cc_final: 0.7481 (mmm)
REVERT: 1  197 PHE cc_start: 0.6170 (m-10) cc_final: 0.5883 (m-10)
REVERT: 1  204 MET cc_start: 0.6232 (tmm) cc_final: 0.5779 (tmt)
REVERT: 1  205 MET cc_start: 0.9010 (ttm) cc_final: 0.8575 (mtt)
REVERT: A  145 GLU cc_start: 0.8432 (mp0) cc_final: 0.7922 (mp0)
REVERT: A  197 PHE cc_start: 0.6396 (m-10) cc_final: 0.5370 (m-10)
REVERT: A  210 GLU cc_start: 0.7715 (mp0) cc_final: 0.7309 (mp0)
REVERT: B  145 GLU cc_start: 0.8421 (mp0) cc_final: 0.8184 (mp0)
REVERT: B  146 ASP cc_start: 0.8319 (t0) cc_final: 0.7847 (t0)
REVERT: B  155 ARG cc_start: 0.7960 (mtt180) cc_final: 0.6192 (mmt-90)
REVERT: B  207 ARG cc_start: 0.7501 (mtt180) cc_final: 0.5724 (tmm160)
REVERT: B  212 MET cc_start: 0.8391 (tpp) cc_final: 0.8131 (ttm)
REVERT: B  219 LYS cc_start: 0.8124 (mttt) cc_final: 0.6512 (pmtt)
REVERT: B  220 GLU cc_start: 0.8295 (mp0) cc_final: 0.7580 (pp20)
REVERT: C  107 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7929 (m-40)
REVERT: C  128 MET cc_start: 0.9111 (mtp) cc_final: 0.8845 (mtp)
REVERT: C  137 MET cc_start: 0.8026 (ttm) cc_final: 0.7624 (ttm)
REVERT: C  195 GLU cc_start: 0.5244 (tm-30) cc_final: 0.4004 (tt0)
REVERT: C  204 MET cc_start: 0.6389 (tmt) cc_final: 0.6069 (tmt)
REVERT: C  210 GLU cc_start: 0.7436 (mp0) cc_final: 0.7009 (tm-30)
REVERT: C  211 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7926 (mt0)
REVERT: C  220 GLU cc_start: 0.8763 (mp0) cc_final: 0.8172 (mp0)
REVERT: C  229 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6721 (mtp85)
REVERT: D  100 LYS cc_start: 0.7722 (mtmt) cc_final: 0.6708 (mmtt)
REVERT: D  133 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6678 (mpt)
REVERT: D  135 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7093 (tpm170)
REVERT: D  140 PHE cc_start: 0.8468 (m-80) cc_final: 0.6062 (p90)
REVERT: D  143 ASP cc_start: 0.8326 (t0) cc_final: 0.7682 (m-30)
REVERT: D  145 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8121 (mt-10)
REVERT: D  146 ASP cc_start: 0.8219 (t0) cc_final: 0.7795 (t0)
REVERT: D  153 MET cc_start: 0.8578 (mmm) cc_final: 0.6464 (pp-130)
REVERT: D  155 ARG cc_start: 0.8314 (mtt180) cc_final: 0.6693 (ptt90)
REVERT: D  163 ARG cc_start: 0.8985 (mtt180) cc_final: 0.6959 (pmt170)
REVERT: D  207 ARG cc_start: 0.8033 (mtt180) cc_final: 0.5808 (mmp-170)
REVERT: D  212 MET cc_start: 0.8808 (tpp) cc_final: 0.6913 (pmt)
REVERT: D  229 ARG cc_start: 0.8258 (mtt180) cc_final: 0.6986 (pmt170)
  outliers start: 14
  outliers final: 6
  residues processed: 153
  average time/residue: 1.6393
  time to fit residues: 258.9190
Evaluate side-chains
  150 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
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  211 GLN
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:    0.0470
   chunk 4 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.3682

-------------------------------------------------------------------------------
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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** 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 = 0.4187 r_free = 0.4187 target = 0.114632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.097922 restraints weight = 9973.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 3.05
r_work: 0.3903 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5710  Z= 0.220
  Angle     :  0.760   9.550   7720  Z= 0.403
  Chirality :  0.050   0.179    780
  Planarity :  0.003   0.029   1020
  Dihedral  :  5.657  23.764    780
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.86 %
    Favored  : 74.62 %
  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   0.008   0.001   TRP A  98 
 HIS   0.003   0.001   HIS 1 110 
 PHE   0.020   0.002   PHE B 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: 5151.69 seconds
wall clock time: 92 minutes 4.80 seconds (5524.80 seconds total)