Starting phenix.real_space_refine
on Thu Jun  5 07:40:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7td6_25824/06_2025/7td6_25824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7td6_25824/06_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_25824/06_2025/7td6_25824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7td6_25824/06_2025/7td6_25824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7td6_25824/06_2025/7td6_25824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7td6_25824/06_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-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5575
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "1"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "A"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1115
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 5, 'TRANS': 132}
  Time building chain proxies: 4.36, per 1000 atoms: 0.78
  Number of scatterers: 5575
  At special positions: 0
  Unit cell: (105.73, 112.27, 53.41, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1060      8.00
     N    1010      7.00
     C    3460      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 698.4 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: 0.83
  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: 1.33

  Time building geometry restraints manager: 1.59 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:             3.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.830
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:16.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.560
-------------------------------------------------------------------------------
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   5715  Z= 0.094
  Angle     :  0.570   5.341   7730  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16179 (   65)
  hydrogen bonds       : angle       7.23685 (  195)
  SS BOND              : bond        0.00027 (    5)
  SS BOND              : angle       0.92263 (   10)
  covalent geometry    : bond        0.00192 ( 5710)
  covalent geometry    : angle       0.56965 ( 7720)

*********************** 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  : 0.656 
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: 1.6056
  time to fit residues: 331.2957
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  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0000
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    8.9990
   overall best weight:    1.6986

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

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

Total number of N/Q/H flips: 9

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5715  Z= 0.146
  Angle     :  0.597   6.478   7730  Z= 0.322
  Chirality :  0.047   0.132    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  4.600  16.761    780
  Min Nonbonded Distance : 2.507

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

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

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02972 (   65)
  hydrogen bonds       : angle       5.39771 (  195)
  SS BOND              : bond        0.00082 (    5)
  SS BOND              : angle       0.57838 (   10)
  covalent geometry    : bond        0.00335 ( 5710)
  covalent geometry    : angle       0.59716 ( 7720)

*********************** 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  : 0.624 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8513 (ptm-80) cc_final: 0.8276 (ptp90)
REVERT: 1  137 MET cc_start: 0.8467 (ttm) cc_final: 0.7994 (ttm)
REVERT: 1  153 MET cc_start: 0.7761 (mmm) cc_final: 0.7489 (mmm)
REVERT: 1  219 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7693 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8613 (mp0) cc_final: 0.8110 (mp0)
REVERT: A  135 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.8171 (ptp90)
REVERT: A  145 GLU cc_start: 0.8361 (mp0) cc_final: 0.8116 (mp0)
REVERT: A  197 PHE cc_start: 0.6788 (m-10) cc_final: 0.5813 (m-80)
REVERT: A  204 MET cc_start: 0.6701 (tmm) cc_final: 0.6395 (tmm)
REVERT: A  229 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7957 (mmt-90)
REVERT: B  135 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.4760 (pmt170)
REVERT: B  151 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7029 (pm20)
REVERT: B  155 ARG cc_start: 0.8451 (mtt180) cc_final: 0.6778 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8705 (t) cc_final: 0.8290 (m)
REVERT: B  212 MET cc_start: 0.8645 (tpp) cc_final: 0.8382 (ttm)
REVERT: B  219 LYS cc_start: 0.8181 (mttt) cc_final: 0.6597 (pmtt)
REVERT: B  220 GLU cc_start: 0.8291 (mp0) cc_final: 0.7543 (pp20)
REVERT: B  221 SER cc_start: 0.8914 (m) cc_final: 0.8457 (m)
REVERT: C  128 MET cc_start: 0.9117 (mtp) cc_final: 0.8887 (mtp)
REVERT: C  137 MET cc_start: 0.8381 (ttm) cc_final: 0.7982 (ttm)
REVERT: C  155 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7709 (mtp85)
REVERT: C  204 MET cc_start: 0.6791 (tmt) cc_final: 0.6350 (tmt)
REVERT: C  220 GLU cc_start: 0.8542 (mp0) cc_final: 0.8316 (mp0)
REVERT: D  100 LYS cc_start: 0.7465 (mtmt) cc_final: 0.6733 (mmtt)
REVERT: D  133 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6790 (mpt)
REVERT: D  135 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7336 (tpm170)
REVERT: D  140 PHE cc_start: 0.7958 (m-80) cc_final: 0.6709 (p90)
REVERT: D  143 ASP cc_start: 0.8474 (t0) cc_final: 0.7994 (m-30)
REVERT: D  153 MET cc_start: 0.8351 (mmm) cc_final: 0.6938 (ptt)
REVERT: D  155 ARG cc_start: 0.8269 (mtt180) cc_final: 0.6762 (ptt-90)
REVERT: D  163 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7290 (pmt170)
REVERT: D  177 ASP cc_start: 0.7882 (m-30) cc_final: 0.7488 (m-30)
REVERT: D  204 MET cc_start: 0.6914 (tmm) cc_final: 0.6636 (tmm)
REVERT: D  206 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7167 (tm-30)
REVERT: D  207 ARG cc_start: 0.8001 (mtt180) cc_final: 0.6513 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8221 (mm-40)
REVERT: D  212 MET cc_start: 0.8689 (tpp) cc_final: 0.6965 (pmt)
REVERT: D  222 GLN cc_start: 0.8683 (mp-120) cc_final: 0.8282 (mp10)
REVERT: D  224 TYR cc_start: 0.7984 (m-80) cc_final: 0.7573 (m-80)
REVERT: D  226 ASP cc_start: 0.7469 (p0) cc_final: 0.7020 (p0)
REVERT: D  229 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7174 (pmt170)
  outliers start: 13
  outliers final: 3
  residues processed: 168
  average time/residue: 1.3914
  time to fit residues: 242.1956
Evaluate side-chains
  163 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    2.8788

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.115121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.099449 restraints weight = 10020.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 3.00
r_work: 0.3933 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5715  Z= 0.210
  Angle     :  0.640   8.206   7730  Z= 0.345
  Chirality :  0.049   0.136    780
  Planarity :  0.003   0.021   1020
  Dihedral  :  5.234  18.816    780
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.64 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.015   0.003   PHE B 174 
 TYR   0.028   0.002   TYR C 217 
 ARG   0.003   0.000   ARG B 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02936 (   65)
  hydrogen bonds       : angle       4.90247 (  195)
  SS BOND              : bond        0.00132 (    5)
  SS BOND              : angle       0.75114 (   10)
  covalent geometry    : bond        0.00464 ( 5710)
  covalent geometry    : angle       0.64006 ( 7720)

*********************** 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
  185 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.633 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8413 (ptm-80) cc_final: 0.7967 (ptp90)
REVERT: 1  137 MET cc_start: 0.8148 (ttm) cc_final: 0.7700 (ttm)
REVERT: 1  153 MET cc_start: 0.7618 (mmm) cc_final: 0.7223 (mmm)
REVERT: 1  197 PHE cc_start: 0.6649 (m-10) cc_final: 0.6213 (m-10)
REVERT: 1  204 MET cc_start: 0.6272 (tmm) cc_final: 0.5799 (tmt)
REVERT: 1  219 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7687 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8620 (mp0) cc_final: 0.8171 (mp0)
REVERT: A  145 GLU cc_start: 0.8427 (mp0) cc_final: 0.8118 (mp0)
REVERT: A  161 TYR cc_start: 0.8864 (m-10) cc_final: 0.8552 (m-80)
REVERT: A  211 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7643 (mt0)
REVERT: B  100 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7916 (mttp)
REVERT: B  155 ARG cc_start: 0.8003 (mtt180) cc_final: 0.6351 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8277 (tp30) cc_final: 0.7399 (tm-30)
REVERT: B  207 ARG cc_start: 0.7579 (mtt180) cc_final: 0.5745 (tmm160)
REVERT: B  212 MET cc_start: 0.8467 (tpp) cc_final: 0.8207 (ttm)
REVERT: B  219 LYS cc_start: 0.8104 (mttt) cc_final: 0.6662 (pmtt)
REVERT: B  220 GLU cc_start: 0.8324 (mp0) cc_final: 0.7508 (pp20)
REVERT: B  228 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.5919 (pmt-80)
REVERT: C  100 LYS cc_start: 0.7482 (mtmt) cc_final: 0.7137 (mttp)
REVERT: C  128 MET cc_start: 0.9094 (mtp) cc_final: 0.8797 (mtp)
REVERT: C  137 MET cc_start: 0.8052 (ttm) cc_final: 0.7569 (ttm)
REVERT: C  155 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7133 (mtt90)
REVERT: C  195 GLU cc_start: 0.4960 (tm-30) cc_final: 0.3912 (tt0)
REVERT: C  204 MET cc_start: 0.6350 (tmt) cc_final: 0.6030 (tmt)
REVERT: C  220 GLU cc_start: 0.8656 (mp0) cc_final: 0.8156 (mp0)
REVERT: D  100 LYS cc_start: 0.7424 (mtmt) cc_final: 0.6586 (mmtt)
REVERT: D  135 ARG cc_start: 0.7908 (mtt180) cc_final: 0.6967 (tpm170)
REVERT: D  140 PHE cc_start: 0.8213 (m-80) cc_final: 0.6532 (p90)
REVERT: D  143 ASP cc_start: 0.8221 (t0) cc_final: 0.7804 (m-30)
REVERT: D  146 ASP cc_start: 0.8055 (t0) cc_final: 0.7792 (t0)
REVERT: D  155 ARG cc_start: 0.8299 (mtt180) cc_final: 0.6724 (ptt90)
REVERT: D  158 ASN cc_start: 0.8682 (m110) cc_final: 0.8420 (m-40)
REVERT: D  163 ARG cc_start: 0.8544 (mtt180) cc_final: 0.6962 (pmt170)
REVERT: D  204 MET cc_start: 0.6565 (tmm) cc_final: 0.6267 (tmm)
REVERT: D  207 ARG cc_start: 0.7916 (mtt180) cc_final: 0.6061 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7753 (mm-40)
REVERT: D  212 MET cc_start: 0.8917 (tpp) cc_final: 0.6941 (pmt)
REVERT: D  221 SER cc_start: 0.8541 (p) cc_final: 0.8005 (m)
REVERT: D  222 GLN cc_start: 0.8376 (mp-120) cc_final: 0.7610 (mm-40)
REVERT: D  224 TYR cc_start: 0.7725 (m-80) cc_final: 0.7376 (m-80)
REVERT: D  229 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7062 (pmt170)
  outliers start: 15
  outliers final: 5
  residues processed: 179
  average time/residue: 1.4538
  time to fit residues: 269.2781
Evaluate side-chains
  162 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  211 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    3.9990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.111280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.095691 restraints weight = 10207.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 2.95
r_work: 0.3874 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   5715  Z= 0.263
  Angle     :  0.680   7.690   7730  Z= 0.369
  Chirality :  0.049   0.142    780
  Planarity :  0.003   0.017   1020
  Dihedral  :  5.629  20.366    780
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 18.49 %
    Favored  : 77.14 %
  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: -3.64 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  98 
 HIS   0.006   0.001   HIS 1 110 
 PHE   0.015   0.003   PHE B 174 
 TYR   0.029   0.003   TYR C 217 
 ARG   0.004   0.000   ARG B 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (   65)
  hydrogen bonds       : angle       4.68485 (  195)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       0.89415 (   10)
  covalent geometry    : bond        0.00591 ( 5710)
  covalent geometry    : angle       0.67937 ( 7720)

*********************** 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
  184 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: 1  135 ARG cc_start: 0.8357 (ptm-80) cc_final: 0.8055 (ptp90)
REVERT: 1  137 MET cc_start: 0.8173 (ttm) cc_final: 0.7823 (ttm)
REVERT: 1  153 MET cc_start: 0.7697 (mmm) cc_final: 0.7366 (mmm)
REVERT: 1  197 PHE cc_start: 0.6205 (m-10) cc_final: 0.5904 (m-10)
REVERT: 1  204 MET cc_start: 0.6176 (tmm) cc_final: 0.5932 (tmt)
REVERT: 1  205 MET cc_start: 0.8889 (ttm) cc_final: 0.8467 (mtm)
REVERT: 1  211 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8588 (mm-40)
REVERT: 1  220 GLU cc_start: 0.8616 (mp0) cc_final: 0.8293 (mp0)
REVERT: A  145 GLU cc_start: 0.8407 (mp0) cc_final: 0.7981 (mp0)
REVERT: A  155 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6908 (mpp80)
REVERT: A  197 PHE cc_start: 0.6289 (m-10) cc_final: 0.5021 (m-10)
REVERT: A  210 GLU cc_start: 0.7735 (mp0) cc_final: 0.7228 (mp0)
REVERT: A  211 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8169 (mt0)
REVERT: B  100 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7730 (mttp)
REVERT: B  135 ARG cc_start: 0.6019 (OUTLIER) cc_final: 0.4896 (pmt170)
REVERT: B  140 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.7135 (m-10)
REVERT: B  146 ASP cc_start: 0.8366 (t0) cc_final: 0.7976 (t0)
REVERT: B  155 ARG cc_start: 0.8048 (mtt180) cc_final: 0.6349 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8193 (tp30) cc_final: 0.7328 (tm-30)
REVERT: B  207 ARG cc_start: 0.7578 (mtt180) cc_final: 0.5834 (tmm160)
REVERT: B  212 MET cc_start: 0.8492 (tpp) cc_final: 0.8213 (ttm)
REVERT: B  219 LYS cc_start: 0.8169 (mttt) cc_final: 0.6484 (pmtt)
REVERT: B  220 GLU cc_start: 0.8327 (mp0) cc_final: 0.7515 (pp20)
REVERT: B  228 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.5974 (pmt-80)
REVERT: C  100 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7161 (mttp)
REVERT: C  128 MET cc_start: 0.9115 (mtp) cc_final: 0.8814 (mtp)
REVERT: C  137 MET cc_start: 0.8106 (ttm) cc_final: 0.7658 (ttm)
REVERT: C  195 GLU cc_start: 0.5035 (tm-30) cc_final: 0.3973 (tt0)
REVERT: C  197 PHE cc_start: 0.6270 (m-10) cc_final: 0.5728 (m-10)
REVERT: C  204 MET cc_start: 0.6454 (tmt) cc_final: 0.6100 (tmt)
REVERT: C  210 GLU cc_start: 0.7532 (mp0) cc_final: 0.6988 (tm-30)
REVERT: C  220 GLU cc_start: 0.8805 (mp0) cc_final: 0.8216 (mp0)
REVERT: D  100 LYS cc_start: 0.7552 (mtmt) cc_final: 0.6607 (mmtt)
REVERT: D  135 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7244 (tpm170)
REVERT: D  140 PHE cc_start: 0.8276 (m-80) cc_final: 0.6324 (p90)
REVERT: D  143 ASP cc_start: 0.8234 (t0) cc_final: 0.7848 (m-30)
REVERT: D  145 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8076 (mt-10)
REVERT: D  146 ASP cc_start: 0.8187 (t0) cc_final: 0.7841 (t0)
REVERT: D  148 TYR cc_start: 0.8249 (p90) cc_final: 0.8001 (p90)
REVERT: D  153 MET cc_start: 0.8562 (mmm) cc_final: 0.6572 (pp-130)
REVERT: D  155 ARG cc_start: 0.8282 (mtt180) cc_final: 0.6714 (ptt90)
REVERT: D  158 ASN cc_start: 0.8744 (m110) cc_final: 0.8469 (m-40)
REVERT: D  163 ARG cc_start: 0.8751 (mtt180) cc_final: 0.7002 (pmt170)
REVERT: D  204 MET cc_start: 0.6647 (tmm) cc_final: 0.6314 (tmm)
REVERT: D  207 ARG cc_start: 0.8048 (mtt180) cc_final: 0.5921 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7950 (mm-40)
REVERT: D  212 MET cc_start: 0.8865 (tpp) cc_final: 0.6976 (pmt)
REVERT: D  221 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8435 (m)
REVERT: D  222 GLN cc_start: 0.8411 (mp-120) cc_final: 0.8008 (mp10)
REVERT: D  224 TYR cc_start: 0.7806 (m-80) cc_final: 0.7437 (m-80)
REVERT: D  229 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7107 (pmt170)
  outliers start: 26
  outliers final: 5
  residues processed: 173
  average time/residue: 1.6754
  time to fit residues: 299.1860
Evaluate side-chains
  161 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  155 ARG
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 172 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.112057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.096388 restraints weight = 9990.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 2.96
r_work: 0.3879 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5715  Z= 0.232
  Angle     :  0.677   7.839   7730  Z= 0.366
  Chirality :  0.049   0.141    780
  Planarity :  0.003   0.018   1020
  Dihedral  :  5.704  21.774    780
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.50 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  98 
 HIS   0.005   0.001   HIS 1 110 
 PHE   0.029   0.003   PHE B 197 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.004   0.000   ARG B 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02931 (   65)
  hydrogen bonds       : angle       4.55587 (  195)
  SS BOND              : bond        0.00116 (    5)
  SS BOND              : angle       0.87562 (   10)
  covalent geometry    : bond        0.00522 ( 5710)
  covalent geometry    : angle       0.67651 ( 7720)

*********************** 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: 21
    poor density    : 158
  time to evaluate  : 1.065 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8379 (ptm-80) cc_final: 0.7944 (ptp90)
REVERT: 1  137 MET cc_start: 0.7999 (ttm) cc_final: 0.7447 (ttm)
REVERT: 1  153 MET cc_start: 0.7688 (mmm) cc_final: 0.7289 (mmm)
REVERT: 1  197 PHE cc_start: 0.6137 (m-10) cc_final: 0.5836 (m-10)
REVERT: 1  204 MET cc_start: 0.5963 (tmm) cc_final: 0.5656 (tmt)
REVERT: 1  211 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8452 (mm-40)
REVERT: A  145 GLU cc_start: 0.8307 (mp0) cc_final: 0.7815 (mp0)
REVERT: A  197 PHE cc_start: 0.6133 (m-10) cc_final: 0.4855 (m-10)
REVERT: A  211 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7595 (mt0)
REVERT: B  100 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7678 (mttp)
REVERT: B  140 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7182 (m-10)
REVERT: B  145 GLU cc_start: 0.8321 (mp0) cc_final: 0.8074 (mp0)
REVERT: B  146 ASP cc_start: 0.8149 (t0) cc_final: 0.7669 (t0)
REVERT: B  155 ARG cc_start: 0.7790 (mtt180) cc_final: 0.6050 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8123 (tp30) cc_final: 0.7643 (tm-30)
REVERT: B  207 ARG cc_start: 0.7455 (mtt180) cc_final: 0.5733 (tmm160)
REVERT: B  212 MET cc_start: 0.8285 (tpp) cc_final: 0.8035 (ttm)
REVERT: B  219 LYS cc_start: 0.8074 (mttt) cc_final: 0.6443 (pmtt)
REVERT: B  220 GLU cc_start: 0.8238 (mp0) cc_final: 0.7576 (pp20)
REVERT: B  228 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.5850 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7788 (m-40)
REVERT: C  128 MET cc_start: 0.9033 (mtp) cc_final: 0.8748 (mtp)
REVERT: C  137 MET cc_start: 0.7890 (ttm) cc_final: 0.7462 (ttm)
REVERT: C  155 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7448 (mtt180)
REVERT: C  197 PHE cc_start: 0.6204 (m-10) cc_final: 0.5974 (m-10)
REVERT: C  204 MET cc_start: 0.6237 (tmt) cc_final: 0.5964 (tmt)
REVERT: C  220 GLU cc_start: 0.8700 (mp0) cc_final: 0.8069 (mp0)
REVERT: D  100 LYS cc_start: 0.7529 (mtmt) cc_final: 0.6593 (mmtt)
REVERT: D  133 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6543 (mpt)
REVERT: D  135 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7135 (tpm170)
REVERT: D  140 PHE cc_start: 0.8369 (m-80) cc_final: 0.6169 (p90)
REVERT: D  143 ASP cc_start: 0.8184 (t0) cc_final: 0.7666 (m-30)
REVERT: D  145 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7924 (mt-10)
REVERT: D  146 ASP cc_start: 0.8035 (t0) cc_final: 0.7676 (t0)
REVERT: D  153 MET cc_start: 0.8566 (mmm) cc_final: 0.6533 (pp-130)
REVERT: D  155 ARG cc_start: 0.8205 (mtt180) cc_final: 0.6550 (ptt90)
REVERT: D  158 ASN cc_start: 0.8610 (m110) cc_final: 0.8315 (m-40)
REVERT: D  163 ARG cc_start: 0.8820 (mtt180) cc_final: 0.6973 (pmt170)
REVERT: D  204 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.6050 (tmm)
REVERT: D  207 ARG cc_start: 0.7939 (mtt180) cc_final: 0.5791 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7762 (mm-40)
REVERT: D  212 MET cc_start: 0.8866 (tpp) cc_final: 0.6976 (pmt)
REVERT: D  221 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8345 (m)
REVERT: D  222 GLN cc_start: 0.8124 (mp-120) cc_final: 0.7757 (mp-120)
REVERT: D  224 TYR cc_start: 0.7568 (m-80) cc_final: 0.7195 (m-80)
REVERT: D  229 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7000 (pmt170)
  outliers start: 21
  outliers final: 6
  residues processed: 169
  average time/residue: 1.8896
  time to fit residues: 329.3725
Evaluate side-chains
  166 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  204 MET
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0670
   chunk 50 optimal weight:    4.9990
   overall best weight:    3.0126

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
B 142 ASN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.111855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.096146 restraints weight = 9976.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 2.98
r_work: 0.3916 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5715  Z= 0.213
  Angle     :  0.691   7.819   7730  Z= 0.370
  Chirality :  0.050   0.153    780
  Planarity :  0.003   0.019   1020
  Dihedral  :  5.708  22.585    780
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 19.33 %
    Favored  : 76.81 %
  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   0.011   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 
 PHE   0.014   0.002   PHE 1 174 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.006   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02800 (   65)
  hydrogen bonds       : angle       4.47005 (  195)
  SS BOND              : bond        0.00105 (    5)
  SS BOND              : angle       0.85429 (   10)
  covalent geometry    : bond        0.00482 ( 5710)
  covalent geometry    : angle       0.69047 ( 7720)

*********************** 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
  176 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.689 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8386 (ptp90)
REVERT: 1  137 MET cc_start: 0.8508 (ttm) cc_final: 0.8219 (ttm)
REVERT: 1  153 MET cc_start: 0.8161 (mmm) cc_final: 0.7838 (mmm)
REVERT: 1  197 PHE cc_start: 0.6544 (m-10) cc_final: 0.6301 (m-10)
REVERT: 1  204 MET cc_start: 0.6760 (tmm) cc_final: 0.6506 (tmt)
REVERT: 1  205 MET cc_start: 0.8975 (ttm) cc_final: 0.8743 (mtm)
REVERT: 1  211 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8700 (mm-40)
REVERT: A  133 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7776 (mtm)
REVERT: A  145 GLU cc_start: 0.8611 (mp0) cc_final: 0.8219 (mp0)
REVERT: A  197 PHE cc_start: 0.6697 (m-10) cc_final: 0.5636 (m-10)
REVERT: A  210 GLU cc_start: 0.8123 (mp0) cc_final: 0.7910 (mp0)
REVERT: A  211 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8174 (mt0)
REVERT: B  100 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8006 (mttp)
REVERT: B  135 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5268 (pmt170)
REVERT: B  140 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7180 (m-10)
REVERT: B  146 ASP cc_start: 0.8593 (t0) cc_final: 0.8353 (t0)
REVERT: B  155 ARG cc_start: 0.8460 (mtt180) cc_final: 0.6777 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8283 (tp30) cc_final: 0.7971 (tm-30)
REVERT: B  207 ARG cc_start: 0.7680 (mtt180) cc_final: 0.5924 (tmm160)
REVERT: B  212 MET cc_start: 0.8579 (tpp) cc_final: 0.8330 (ttm)
REVERT: B  219 LYS cc_start: 0.8304 (mttt) cc_final: 0.6702 (pmtt)
REVERT: B  220 GLU cc_start: 0.8275 (mp0) cc_final: 0.7659 (pp20)
REVERT: B  228 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.6138 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8299 (m-40)
REVERT: C  128 MET cc_start: 0.9189 (mtp) cc_final: 0.8979 (mtp)
REVERT: C  137 MET cc_start: 0.8456 (ttm) cc_final: 0.8101 (ttm)
REVERT: C  195 GLU cc_start: 0.5145 (tm-30) cc_final: 0.4448 (tt0)
REVERT: C  204 MET cc_start: 0.6843 (tmt) cc_final: 0.6552 (tmt)
REVERT: C  211 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8091 (mt0)
REVERT: C  220 GLU cc_start: 0.8881 (mp0) cc_final: 0.8359 (mp0)
REVERT: C  229 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7026 (mtp85)
REVERT: D  100 LYS cc_start: 0.7923 (mtmt) cc_final: 0.6987 (mmtt)
REVERT: D  133 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7133 (mpt)
REVERT: D  135 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7544 (tpm170)
REVERT: D  140 PHE cc_start: 0.8260 (m-80) cc_final: 0.6280 (p90)
REVERT: D  143 ASP cc_start: 0.8364 (t0) cc_final: 0.8052 (m-30)
REVERT: D  145 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8330 (mt-10)
REVERT: D  146 ASP cc_start: 0.8468 (t0) cc_final: 0.8085 (t0)
REVERT: D  153 MET cc_start: 0.8670 (mmm) cc_final: 0.6675 (pp-130)
REVERT: D  155 ARG cc_start: 0.8392 (mtt180) cc_final: 0.7086 (ptt90)
REVERT: D  163 ARG cc_start: 0.8902 (mtt180) cc_final: 0.7194 (pmt170)
REVERT: D  204 MET cc_start: 0.6934 (tmm) cc_final: 0.6585 (tmm)
REVERT: D  207 ARG cc_start: 0.8350 (mtt180) cc_final: 0.6133 (mmp-170)
REVERT: D  212 MET cc_start: 0.8798 (tpp) cc_final: 0.7153 (pmt)
REVERT: D  222 GLN cc_start: 0.8743 (mp-120) cc_final: 0.8377 (mp-120)
REVERT: D  229 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7170 (pmt170)
  outliers start: 23
  outliers final: 6
  residues processed: 165
  average time/residue: 1.5515
  time to fit residues: 264.3146
Evaluate side-chains
  160 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  108 LEU
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0970
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    0.9180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.114826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.099497 restraints weight = 9868.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 3.00
r_work: 0.3941 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5715  Z= 0.129
  Angle     :  0.672   7.774   7730  Z= 0.359
  Chirality :  0.049   0.154    780
  Planarity :  0.003   0.025   1020
  Dihedral  :  5.498  22.853    780
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.84 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  98 
 HIS   0.002   0.001   HIS D 110 
 PHE   0.022   0.003   PHE B 197 
 TYR   0.029   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02151 (   65)
  hydrogen bonds       : angle       4.32166 (  195)
  SS BOND              : bond        0.00137 (    5)
  SS BOND              : angle       0.75203 (   10)
  covalent geometry    : bond        0.00296 ( 5710)
  covalent geometry    : angle       0.67223 ( 7720)

*********************** 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
  171 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.724 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.7999 (ptp90)
REVERT: 1  137 MET cc_start: 0.8109 (ttm) cc_final: 0.7543 (ttm)
REVERT: 1  153 MET cc_start: 0.7698 (mmm) cc_final: 0.7366 (mmm)
REVERT: 1  197 PHE cc_start: 0.6148 (m-10) cc_final: 0.5843 (m-10)
REVERT: 1  204 MET cc_start: 0.6235 (tmm) cc_final: 0.5960 (tmt)
REVERT: 1  205 MET cc_start: 0.8731 (ttm) cc_final: 0.8492 (mtm)
REVERT: A  133 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7279 (mtm)
REVERT: A  145 GLU cc_start: 0.8423 (mp0) cc_final: 0.7942 (mp0)
REVERT: A  195 GLU cc_start: 0.6063 (tm-30) cc_final: 0.5355 (tm-30)
REVERT: A  197 PHE cc_start: 0.6069 (m-10) cc_final: 0.4988 (m-10)
REVERT: B  100 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7685 (mttp)
REVERT: B  140 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7100 (m-10)
REVERT: B  146 ASP cc_start: 0.8217 (t0) cc_final: 0.7799 (t0)
REVERT: B  155 ARG cc_start: 0.7958 (mtt180) cc_final: 0.6280 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8702 (t) cc_final: 0.8286 (m)
REVERT: B  206 GLU cc_start: 0.8177 (tp30) cc_final: 0.7552 (tm-30)
REVERT: B  207 ARG cc_start: 0.7534 (mtt180) cc_final: 0.5621 (tmm160)
REVERT: B  212 MET cc_start: 0.8330 (tpp) cc_final: 0.8051 (ttm)
REVERT: B  219 LYS cc_start: 0.8049 (mttt) cc_final: 0.6504 (pmtt)
REVERT: B  220 GLU cc_start: 0.8331 (mp0) cc_final: 0.7566 (pp20)
REVERT: B  228 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.5937 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7782 (m-40)
REVERT: C  128 MET cc_start: 0.9057 (mtp) cc_final: 0.8793 (mtp)
REVERT: C  137 MET cc_start: 0.7995 (ttm) cc_final: 0.7595 (ttm)
REVERT: C  195 GLU cc_start: 0.5061 (tm-30) cc_final: 0.4085 (tt0)
REVERT: C  197 PHE cc_start: 0.6017 (m-10) cc_final: 0.5256 (m-10)
REVERT: C  204 MET cc_start: 0.6241 (tmt) cc_final: 0.5896 (tmt)
REVERT: C  210 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6556 (tm-30)
REVERT: C  220 GLU cc_start: 0.8692 (mp0) cc_final: 0.8082 (mp0)
REVERT: C  229 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.6717 (mtp85)
REVERT: D  100 LYS cc_start: 0.7662 (mtmt) cc_final: 0.6643 (mmtt)
REVERT: D  133 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6663 (mpt)
REVERT: D  135 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7107 (tpm170)
REVERT: D  140 PHE cc_start: 0.8425 (m-80) cc_final: 0.6271 (p90)
REVERT: D  143 ASP cc_start: 0.8228 (t0) cc_final: 0.7684 (m-30)
REVERT: D  145 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7925 (mt-10)
REVERT: D  146 ASP cc_start: 0.8072 (t0) cc_final: 0.7673 (t0)
REVERT: D  153 MET cc_start: 0.8605 (mmm) cc_final: 0.6507 (pp-130)
REVERT: D  155 ARG cc_start: 0.8197 (mtt180) cc_final: 0.6719 (ptt90)
REVERT: D  163 ARG cc_start: 0.8893 (mtt180) cc_final: 0.6977 (pmt170)
REVERT: D  207 ARG cc_start: 0.8056 (mtt180) cc_final: 0.5916 (mmp-170)
REVERT: D  212 MET cc_start: 0.8858 (tpp) cc_final: 0.6976 (pmt)
REVERT: D  219 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7348 (tptt)
REVERT: D  222 GLN cc_start: 0.8312 (mp-120) cc_final: 0.7930 (mp-120)
REVERT: D  229 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7044 (pmt170)
  outliers start: 20
  outliers final: 3
  residues processed: 158
  average time/residue: 1.5498
  time to fit residues: 253.1346
Evaluate side-chains
  149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.111983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.095362 restraints weight = 10019.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 2.99
r_work: 0.3884 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.4211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5715  Z= 0.223
  Angle     :  0.728   8.088   7730  Z= 0.390
  Chirality :  0.050   0.145    780
  Planarity :  0.003   0.022   1020
  Dihedral  :  5.731  23.940    780
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.18 %
    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: -3.78 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (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   0.015   0.003   PHE 1 174 
 TYR   0.031   0.002   TYR C 217 
 ARG   0.007   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02709 (   65)
  hydrogen bonds       : angle       4.34415 (  195)
  SS BOND              : bond        0.00089 (    5)
  SS BOND              : angle       0.94893 (   10)
  covalent geometry    : bond        0.00504 ( 5710)
  covalent geometry    : angle       0.72734 ( 7720)

*********************** 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
  168 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.637 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.7964 (ptp90)
REVERT: 1  137 MET cc_start: 0.8003 (ttm) cc_final: 0.7625 (ttm)
REVERT: 1  153 MET cc_start: 0.7757 (mmm) cc_final: 0.7410 (mmm)
REVERT: 1  197 PHE cc_start: 0.6173 (m-10) cc_final: 0.5880 (m-10)
REVERT: 1  204 MET cc_start: 0.6266 (tmm) cc_final: 0.6027 (tmt)
REVERT: 1  205 MET cc_start: 0.8775 (ttm) cc_final: 0.8499 (mtm)
REVERT: A  133 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7260 (mtm)
REVERT: A  145 GLU cc_start: 0.8401 (mp0) cc_final: 0.7911 (mp0)
REVERT: A  197 PHE cc_start: 0.6198 (m-10) cc_final: 0.5045 (m-10)
REVERT: A  217 TYR cc_start: 0.8343 (p90) cc_final: 0.8138 (p90)
REVERT: A  226 ASP cc_start: 0.7218 (p0) cc_final: 0.6989 (p0)
REVERT: B  100 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7619 (mttp)
REVERT: B  140 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7189 (m-10)
REVERT: B  145 GLU cc_start: 0.8416 (mp0) cc_final: 0.8211 (mp0)
REVERT: B  146 ASP cc_start: 0.8277 (t0) cc_final: 0.7823 (t0)
REVERT: B  155 ARG cc_start: 0.7887 (mtt180) cc_final: 0.6115 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8143 (tp30) cc_final: 0.7628 (tm-30)
REVERT: B  207 ARG cc_start: 0.7513 (mtt180) cc_final: 0.5705 (tmm160)
REVERT: B  212 MET cc_start: 0.8307 (tpp) cc_final: 0.8038 (ttm)
REVERT: B  219 LYS cc_start: 0.8092 (mttt) cc_final: 0.6474 (pmtt)
REVERT: B  220 GLU cc_start: 0.8308 (mp0) cc_final: 0.7567 (pp20)
REVERT: B  228 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.5951 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7857 (m-40)
REVERT: C  128 MET cc_start: 0.9054 (mtp) cc_final: 0.8802 (mtp)
REVERT: C  137 MET cc_start: 0.7912 (ttm) cc_final: 0.7448 (ttm)
REVERT: C  147 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7754 (ptp-110)
REVERT: C  195 GLU cc_start: 0.5056 (tm-30) cc_final: 0.4314 (tt0)
REVERT: C  204 MET cc_start: 0.6346 (tmt) cc_final: 0.6076 (tmt)
REVERT: C  210 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6853 (tm-30)
REVERT: C  220 GLU cc_start: 0.8767 (mp0) cc_final: 0.8100 (mp0)
REVERT: C  229 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.6758 (mtp85)
REVERT: D  100 LYS cc_start: 0.7675 (mtmt) cc_final: 0.6649 (mmtt)
REVERT: D  133 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6651 (mpt)
REVERT: D  135 ARG cc_start: 0.7856 (mtt180) cc_final: 0.6997 (tpm170)
REVERT: D  140 PHE cc_start: 0.8403 (m-80) cc_final: 0.6134 (p90)
REVERT: D  143 ASP cc_start: 0.8284 (t0) cc_final: 0.7686 (m-30)
REVERT: D  145 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8041 (mt-10)
REVERT: D  146 ASP cc_start: 0.8129 (t0) cc_final: 0.7674 (t0)
REVERT: D  153 MET cc_start: 0.8538 (mmm) cc_final: 0.6508 (pp-130)
REVERT: D  155 ARG cc_start: 0.8293 (mtt180) cc_final: 0.6648 (ptt90)
REVERT: D  163 ARG cc_start: 0.8929 (mtt180) cc_final: 0.6966 (pmt170)
REVERT: D  207 ARG cc_start: 0.8013 (mtt180) cc_final: 0.5837 (mmp-170)
REVERT: D  212 MET cc_start: 0.8847 (tpp) cc_final: 0.6935 (pmt)
REVERT: D  222 GLN cc_start: 0.8327 (mp-120) cc_final: 0.8001 (mp10)
REVERT: D  229 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7038 (pmt170)
  outliers start: 16
  outliers final: 5
  residues processed: 158
  average time/residue: 1.6042
  time to fit residues: 261.4167
Evaluate side-chains
  155 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.1786

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.115742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.099393 restraints weight = 9878.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 3.03
r_work: 0.3906 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5715  Z= 0.139
  Angle     :  0.718   8.252   7730  Z= 0.382
  Chirality :  0.050   0.139    780
  Planarity :  0.003   0.026   1020
  Dihedral  :  5.586  23.550    780
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.51 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.80 (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   0.008   0.001   TRP A  98 
 HIS   0.002   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02072 (   65)
  hydrogen bonds       : angle       4.25688 (  195)
  SS BOND              : bond        0.00119 (    5)
  SS BOND              : angle       0.70819 (   10)
  covalent geometry    : bond        0.00319 ( 5710)
  covalent geometry    : angle       0.71770 ( 7720)

*********************** 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
  172 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.676 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.8066 (ptp90)
REVERT: 1  137 MET cc_start: 0.8180 (ttm) cc_final: 0.7625 (ttm)
REVERT: 1  153 MET cc_start: 0.7804 (mmm) cc_final: 0.7463 (mmm)
REVERT: 1  197 PHE cc_start: 0.6220 (m-10) cc_final: 0.5872 (m-10)
REVERT: 1  204 MET cc_start: 0.6299 (tmm) cc_final: 0.5951 (tmt)
REVERT: 1  205 MET cc_start: 0.8954 (ttm) cc_final: 0.8740 (mtp)
REVERT: A  133 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7402 (mtm)
REVERT: A  145 GLU cc_start: 0.8539 (mp0) cc_final: 0.8010 (mp0)
REVERT: A  197 PHE cc_start: 0.6327 (m-10) cc_final: 0.5241 (m-10)
REVERT: A  211 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7564 (mt0)
REVERT: A  226 ASP cc_start: 0.7411 (p0) cc_final: 0.7017 (p0)
REVERT: B  100 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7656 (mttp)
REVERT: B  140 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7151 (m-10)
REVERT: B  145 GLU cc_start: 0.8392 (mp0) cc_final: 0.8128 (mp0)
REVERT: B  146 ASP cc_start: 0.8350 (t0) cc_final: 0.7902 (t0)
REVERT: B  149 TYR cc_start: 0.7645 (t80) cc_final: 0.6888 (t80)
REVERT: B  155 ARG cc_start: 0.8109 (mtt180) cc_final: 0.6476 (mmp-170)
REVERT: B  161 TYR cc_start: 0.8370 (m-10) cc_final: 0.8007 (m-10)
REVERT: B  175 VAL cc_start: 0.8840 (t) cc_final: 0.8439 (m)
REVERT: B  212 MET cc_start: 0.8411 (tpp) cc_final: 0.8191 (ttm)
REVERT: B  219 LYS cc_start: 0.8098 (mttt) cc_final: 0.6535 (pmtt)
REVERT: B  220 GLU cc_start: 0.8261 (mp0) cc_final: 0.7577 (pp20)
REVERT: B  228 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.5966 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7873 (m-40)
REVERT: C  128 MET cc_start: 0.9104 (mtp) cc_final: 0.8861 (mtp)
REVERT: C  137 MET cc_start: 0.8078 (ttm) cc_final: 0.7683 (ttm)
REVERT: C  195 GLU cc_start: 0.5318 (tm-30) cc_final: 0.4330 (tt0)
REVERT: C  197 PHE cc_start: 0.6025 (m-10) cc_final: 0.5225 (m-10)
REVERT: C  204 MET cc_start: 0.6396 (tmt) cc_final: 0.6124 (tmt)
REVERT: C  220 GLU cc_start: 0.8790 (mp0) cc_final: 0.8134 (mp0)
REVERT: C  229 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6804 (mtp85)
REVERT: D  100 LYS cc_start: 0.7737 (mtmt) cc_final: 0.6739 (mmtt)
REVERT: D  135 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7128 (tpm170)
REVERT: D  140 PHE cc_start: 0.8454 (m-80) cc_final: 0.6247 (p90)
REVERT: D  143 ASP cc_start: 0.8280 (t0) cc_final: 0.7722 (m-30)
REVERT: D  145 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8077 (mt-10)
REVERT: D  146 ASP cc_start: 0.8158 (t0) cc_final: 0.7749 (t0)
REVERT: D  152 ASN cc_start: 0.8566 (m-40) cc_final: 0.7972 (m110)
REVERT: D  153 MET cc_start: 0.8638 (mmm) cc_final: 0.6433 (pp-130)
REVERT: D  155 ARG cc_start: 0.8338 (mtt180) cc_final: 0.6750 (ptt90)
REVERT: D  163 ARG cc_start: 0.8935 (mtt180) cc_final: 0.6986 (pmt170)
REVERT: D  177 ASP cc_start: 0.8032 (m-30) cc_final: 0.7688 (m-30)
REVERT: D  207 ARG cc_start: 0.8158 (mtt180) cc_final: 0.5965 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8389 (mm110) cc_final: 0.7801 (mt0)
REVERT: D  212 MET cc_start: 0.8833 (tpp) cc_final: 0.6962 (pmt)
REVERT: D  222 GLN cc_start: 0.8533 (mp-120) cc_final: 0.8109 (mp10)
REVERT: D  229 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7047 (pmt170)
  outliers start: 19
  outliers final: 5
  residues processed: 163
  average time/residue: 1.6205
  time to fit residues: 273.2015
Evaluate side-chains
  151 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
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  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:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    8.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.111765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.095113 restraints weight = 10065.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 3.00
r_work: 0.3845 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   5715  Z= 0.271
  Angle     :  0.812   8.956   7730  Z= 0.432
  Chirality :  0.051   0.162    780
  Planarity :  0.003   0.024   1020
  Dihedral  :  5.922  24.278    780
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.03 %
    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: -3.86 (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   0.006   0.001   TRP 1  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   0.008   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02860 (   65)
  hydrogen bonds       : angle       4.32510 (  195)
  SS BOND              : bond        0.00111 (    5)
  SS BOND              : angle       1.04078 (   10)
  covalent geometry    : bond        0.00613 ( 5710)
  covalent geometry    : angle       0.81135 ( 7720)

********************** 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
  158 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.657 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8588 (ptm-80) cc_final: 0.8155 (ptp90)
REVERT: 1  137 MET cc_start: 0.8262 (ttm) cc_final: 0.7704 (ttm)
REVERT: 1  153 MET cc_start: 0.7955 (mmm) cc_final: 0.7625 (mmm)
REVERT: 1  197 PHE cc_start: 0.6284 (m-10) cc_final: 0.6020 (m-10)
REVERT: 1  204 MET cc_start: 0.6422 (tmm) cc_final: 0.6061 (tmt)
REVERT: 1  205 MET cc_start: 0.9024 (ttm) cc_final: 0.8744 (mtm)
REVERT: A  133 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7488 (mtm)
REVERT: A  135 ARG cc_start: 0.8598 (ptp-170) cc_final: 0.8319 (ptp90)
REVERT: A  145 GLU cc_start: 0.8564 (mp0) cc_final: 0.8115 (mp0)
REVERT: A  197 PHE cc_start: 0.6503 (m-10) cc_final: 0.5489 (m-10)
REVERT: A  226 ASP cc_start: 0.7496 (p0) cc_final: 0.7218 (p0)
REVERT: B  140 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7171 (m-10)
REVERT: B  145 GLU cc_start: 0.8496 (mp0) cc_final: 0.8266 (mp0)
REVERT: B  146 ASP cc_start: 0.8458 (t0) cc_final: 0.7999 (t0)
REVERT: B  155 ARG cc_start: 0.8164 (mtt180) cc_final: 0.6413 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: B  207 ARG cc_start: 0.7835 (mtt180) cc_final: 0.5825 (tmm160)
REVERT: B  212 MET cc_start: 0.8464 (tpp) cc_final: 0.8183 (ttm)
REVERT: B  219 LYS cc_start: 0.8177 (mttt) cc_final: 0.6555 (pmtt)
REVERT: B  220 GLU cc_start: 0.8338 (mp0) cc_final: 0.7594 (pp20)
REVERT: B  228 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.5993 (pmt-80)
REVERT: C  107 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8121 (m-40)
REVERT: C  128 MET cc_start: 0.9172 (mtp) cc_final: 0.8948 (mtp)
REVERT: C  137 MET cc_start: 0.8223 (ttm) cc_final: 0.7784 (ttm)
REVERT: C  163 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8737 (mtp180)
REVERT: C  195 GLU cc_start: 0.5351 (tm-30) cc_final: 0.4492 (tt0)
REVERT: C  204 MET cc_start: 0.6623 (tmt) cc_final: 0.6259 (tmt)
REVERT: C  220 GLU cc_start: 0.8877 (mp0) cc_final: 0.8246 (mp0)
REVERT: C  229 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6787 (mtp85)
REVERT: D  100 LYS cc_start: 0.7859 (mtmt) cc_final: 0.6845 (mmtt)
REVERT: D  135 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7258 (tpm170)
REVERT: D  140 PHE cc_start: 0.8374 (m-80) cc_final: 0.6094 (p90)
REVERT: D  143 ASP cc_start: 0.8382 (t0) cc_final: 0.7874 (m-30)
REVERT: D  145 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8186 (mt-10)
REVERT: D  153 MET cc_start: 0.8582 (mmm) cc_final: 0.6496 (pp-130)
REVERT: D  155 ARG cc_start: 0.8361 (mtt180) cc_final: 0.6829 (ptt90)
REVERT: D  163 ARG cc_start: 0.9003 (mtt180) cc_final: 0.7074 (pmt170)
REVERT: D  207 ARG cc_start: 0.8203 (mtt180) cc_final: 0.5993 (mmp-170)
REVERT: D  212 MET cc_start: 0.8857 (tpp) cc_final: 0.7029 (pmt)
REVERT: D  229 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7029 (pmt170)
  outliers start: 14
  outliers final: 4
  residues processed: 151
  average time/residue: 1.8319
  time to fit residues: 286.2722
Evaluate side-chains
  151 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  163 ARG
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  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** 1 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 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 = 0.4196 r_free = 0.4196 target = 0.115757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.099358 restraints weight = 9896.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 2.97
r_work: 0.3909 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5715  Z= 0.154
  Angle     :  0.776   9.268   7730  Z= 0.410
  Chirality :  0.050   0.155    780
  Planarity :  0.003   0.029   1020
  Dihedral  :  5.714  23.699    780
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 23.87 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.87 (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   0.009   0.001   TRP A  98 
 HIS   0.002   0.001   HIS 1 110 
 PHE   0.019   0.002   PHE B 197 
 TYR   0.028   0.002   TYR C 217 
 ARG   0.008   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02116 (   65)
  hydrogen bonds       : angle       4.25255 (  195)
  SS BOND              : bond        0.00093 (    5)
  SS BOND              : angle       0.75357 (   10)
  covalent geometry    : bond        0.00355 ( 5710)
  covalent geometry    : angle       0.77609 ( 7720)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6138.40 seconds
wall clock time: 108 minutes 26.37 seconds (6506.37 seconds total)