Starting phenix.real_space_refine
on Fri Aug 22 16:09:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7td6_25824/08_2025/7td6_25824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7td6_25824/08_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_25824/08_2025/7td6_25824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7td6_25824/08_2025/7td6_25824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7td6_25824/08_2025/7td6_25824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7td6_25824/08_2025/7td6_25824.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.53, per 1000 atoms: 0.27
  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: 0.33
  Conformation dependent library (CDL) restraints added in 157.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.20
  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: 0.61

  Time building geometry restraints manager: 0.47 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain '1'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             3.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.230
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.600
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG C 155 
 TYR   0.010   0.001   TYR B 217 
 PHE   0.009   0.001   PHE B 174 
 TRP   0.002   0.001   TRP C 144 
 HIS   0.001   0.000   HIS A 110 

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

*********************** 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  : 0.233 
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: 0.6430
  time to fit residues: 132.6789
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  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0370
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   overall best weight:    2.9464

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.115830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.100953 restraints weight = 10307.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 2.76
r_work: 0.3934 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3833 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5715  Z= 0.207
  Angle     :  0.643   6.771   7730  Z= 0.349
  Chirality :  0.049   0.141    780
  Planarity :  0.003   0.017   1020
  Dihedral  :  4.958  18.151    780
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.94 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.26), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 135 
 TYR   0.027   0.002   TYR C 217 
 PHE   0.016   0.003   PHE 1 197 
 TRP   0.006   0.001   TRP 1 144 
 HIS   0.004   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 5710)
  covalent geometry    : angle       0.64318 ( 7720)
  SS BOND              : bond        0.00166 (    5)
  SS BOND              : angle       0.75245 (   10)
  hydrogen bonds       : bond        0.03048 (   65)
  hydrogen bonds       : angle       5.23364 (  195)

*********************** 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
  177 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.232 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8659 (ptm-80) cc_final: 0.8391 (ptp90)
REVERT: 1  137 MET cc_start: 0.8617 (ttm) cc_final: 0.8230 (ttm)
REVERT: 1  153 MET cc_start: 0.7928 (mmm) cc_final: 0.7588 (mmm)
REVERT: 1  219 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8069 (ttmm)
REVERT: 1  220 GLU cc_start: 0.8689 (mp0) cc_final: 0.8213 (mp0)
REVERT: 1  226 ASP cc_start: 0.7816 (m-30) cc_final: 0.7581 (t0)
REVERT: A  197 PHE cc_start: 0.6913 (m-10) cc_final: 0.5873 (m-80)
REVERT: A  204 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6768 (tmm)
REVERT: B  100 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8065 (mttp)
REVERT: B  105 LYS cc_start: 0.8462 (mttt) cc_final: 0.8248 (mttm)
REVERT: B  145 GLU cc_start: 0.8486 (mp0) cc_final: 0.8257 (mp0)
REVERT: B  155 ARG cc_start: 0.8568 (mtt180) cc_final: 0.6956 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8148 (tp30) cc_final: 0.7711 (tm-30)
REVERT: B  207 ARG cc_start: 0.7698 (mtt180) cc_final: 0.5847 (tmm160)
REVERT: B  212 MET cc_start: 0.8786 (tpp) cc_final: 0.8551 (ttm)
REVERT: B  219 LYS cc_start: 0.8318 (mttt) cc_final: 0.6923 (pmtt)
REVERT: B  220 GLU cc_start: 0.8333 (mp0) cc_final: 0.7527 (pp20)
REVERT: C  100 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7495 (mttp)
REVERT: C  137 MET cc_start: 0.8584 (ttm) cc_final: 0.8252 (ttm)
REVERT: C  148 TYR cc_start: 0.8665 (p90) cc_final: 0.8278 (p90)
REVERT: C  155 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8086 (mtt180)
REVERT: C  204 MET cc_start: 0.7010 (tmt) cc_final: 0.6570 (tmt)
REVERT: C  220 GLU cc_start: 0.8704 (mp0) cc_final: 0.8417 (mp0)
REVERT: C  226 ASP cc_start: 0.7641 (m-30) cc_final: 0.7379 (t0)
REVERT: D  100 LYS cc_start: 0.7745 (mtmt) cc_final: 0.6980 (mmtt)
REVERT: D  133 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7026 (mpt)
REVERT: D  135 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7320 (tpm170)
REVERT: D  140 PHE cc_start: 0.8124 (m-80) cc_final: 0.6712 (p90)
REVERT: D  143 ASP cc_start: 0.8533 (t0) cc_final: 0.8103 (m-30)
REVERT: D  148 TYR cc_start: 0.8472 (p90) cc_final: 0.4404 (t80)
REVERT: D  155 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7164 (ptt90)
REVERT: D  163 ARG cc_start: 0.8605 (mtt180) cc_final: 0.7297 (pmt170)
REVERT: D  204 MET cc_start: 0.7142 (tmm) cc_final: 0.6791 (tmm)
REVERT: D  206 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7524 (tm-30)
REVERT: D  207 ARG cc_start: 0.8124 (mtt180) cc_final: 0.6553 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8343 (mm-40)
REVERT: D  212 MET cc_start: 0.8920 (tpp) cc_final: 0.7050 (pmt)
REVERT: D  221 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8517 (m)
REVERT: D  222 GLN cc_start: 0.8741 (mp-120) cc_final: 0.8330 (mp10)
REVERT: D  226 ASP cc_start: 0.7688 (p0) cc_final: 0.7397 (p0)
REVERT: D  229 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7298 (pmt170)
  outliers start: 17
  outliers final: 3
  residues processed: 166
  average time/residue: 0.6314
  time to fit residues: 108.2572
Evaluate side-chains
  149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
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  204 MET
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 1 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 172 ASN
** 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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN
** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.113067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.097368 restraints weight = 10025.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.96
r_work: 0.3895 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   5715  Z= 0.245
  Angle     :  0.660   7.552   7730  Z= 0.357
  Chirality :  0.049   0.139    780
  Planarity :  0.003   0.017   1020
  Dihedral  :  5.401  19.778    780
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.64 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 135 
 TYR   0.027   0.002   TYR C 217 
 PHE   0.016   0.003   PHE D 174 
 TRP   0.006   0.001   TRP B  98 
 HIS   0.005   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 5710)
  covalent geometry    : angle       0.65972 ( 7720)
  SS BOND              : bond        0.00179 (    5)
  SS BOND              : angle       0.83324 (   10)
  hydrogen bonds       : bond        0.03181 (   65)
  hydrogen bonds       : angle       4.87055 (  195)

*********************** 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
  167 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.140 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8414 (ptm-80) cc_final: 0.7963 (ptp90)
REVERT: 1  137 MET cc_start: 0.8143 (ttm) cc_final: 0.7581 (ttm)
REVERT: 1  153 MET cc_start: 0.7638 (mmm) cc_final: 0.7227 (mmm)
REVERT: 1  197 PHE cc_start: 0.6528 (m-10) cc_final: 0.6108 (m-10)
REVERT: 1  205 MET cc_start: 0.8930 (ttm) cc_final: 0.8423 (mtt)
REVERT: 1  211 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8522 (mm-40)
REVERT: 1  220 GLU cc_start: 0.8592 (mp0) cc_final: 0.8175 (mp0)
REVERT: 1  226 ASP cc_start: 0.7777 (m-30) cc_final: 0.7282 (t0)
REVERT: A  155 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7121 (mpt-90)
REVERT: A  197 PHE cc_start: 0.6363 (m-10) cc_final: 0.5030 (m-10)
REVERT: A  204 MET cc_start: 0.6282 (tmm) cc_final: 0.5947 (tmm)
REVERT: A  211 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7615 (mt0)
REVERT: A  226 ASP cc_start: 0.7400 (p0) cc_final: 0.6917 (p0)
REVERT: B  100 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7909 (mttp)
REVERT: B  135 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.4785 (pmt170)
REVERT: B  145 GLU cc_start: 0.8365 (mp0) cc_final: 0.8059 (mp0)
REVERT: B  155 ARG cc_start: 0.7990 (mtt180) cc_final: 0.6311 (mmp-170)
REVERT: B  193 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7510 (mptt)
REVERT: B  206 GLU cc_start: 0.8276 (tp30) cc_final: 0.7441 (tm-30)
REVERT: B  207 ARG cc_start: 0.7559 (mtt180) cc_final: 0.5814 (tmm160)
REVERT: B  212 MET cc_start: 0.8504 (tpp) cc_final: 0.8226 (ttm)
REVERT: B  219 LYS cc_start: 0.8106 (mttt) cc_final: 0.6484 (pmtt)
REVERT: B  220 GLU cc_start: 0.8356 (mp0) cc_final: 0.7532 (pp20)
REVERT: C  137 MET cc_start: 0.8082 (ttm) cc_final: 0.7644 (ttm)
REVERT: C  155 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7470 (mtt180)
REVERT: C  195 GLU cc_start: 0.5094 (tm-30) cc_final: 0.4005 (tt0)
REVERT: C  197 PHE cc_start: 0.6328 (m-10) cc_final: 0.5720 (m-10)
REVERT: C  204 MET cc_start: 0.6410 (tmt) cc_final: 0.6139 (tmt)
REVERT: C  220 GLU cc_start: 0.8771 (mp0) cc_final: 0.8180 (mp0)
REVERT: C  226 ASP cc_start: 0.7406 (m-30) cc_final: 0.7085 (t0)
REVERT: D  100 LYS cc_start: 0.7472 (mtmt) cc_final: 0.6655 (mmtt)
REVERT: D  135 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7084 (tpm170)
REVERT: D  140 PHE cc_start: 0.8218 (m-80) cc_final: 0.6325 (p90)
REVERT: D  143 ASP cc_start: 0.8257 (t0) cc_final: 0.7806 (m-30)
REVERT: D  153 MET cc_start: 0.8578 (mmm) cc_final: 0.6510 (pp-130)
REVERT: D  155 ARG cc_start: 0.8281 (mtt180) cc_final: 0.6678 (ptt90)
REVERT: D  163 ARG cc_start: 0.8651 (mtt180) cc_final: 0.6968 (pmt170)
REVERT: D  204 MET cc_start: 0.6600 (tmm) cc_final: 0.6234 (tmm)
REVERT: D  207 ARG cc_start: 0.7928 (mtt180) cc_final: 0.6015 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7823 (mm-40)
REVERT: D  212 MET cc_start: 0.8860 (tpp) cc_final: 0.6934 (pmt)
REVERT: D  221 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8468 (m)
REVERT: D  222 GLN cc_start: 0.8366 (mp-120) cc_final: 0.7998 (mp-120)
REVERT: D  226 ASP cc_start: 0.7665 (p0) cc_final: 0.7318 (p0)
REVERT: D  229 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7081 (pmt170)
  outliers start: 18
  outliers final: 4
  residues processed: 158
  average time/residue: 0.6699
  time to fit residues: 108.9447
Evaluate side-chains
  152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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 C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** 1 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 211 GLN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 GLN
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 ASN ** 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 = 0.4172 r_free = 0.4172 target = 0.112538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.096963 restraints weight = 9904.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 2.89
r_work: 0.3890 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5715  Z= 0.205
  Angle     :  0.641   7.710   7730  Z= 0.345
  Chirality :  0.048   0.137    780
  Planarity :  0.003   0.017   1020
  Dihedral  :  5.507  20.390    780
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.48 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.63 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 135 
 TYR   0.029   0.002   TYR C 217 
 PHE   0.015   0.003   PHE B 174 
 TRP   0.008   0.001   TRP A  98 
 HIS   0.004   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 5710)
  covalent geometry    : angle       0.64034 ( 7720)
  SS BOND              : bond        0.00118 (    5)
  SS BOND              : angle       0.83756 (   10)
  hydrogen bonds       : bond        0.02864 (   65)
  hydrogen bonds       : angle       4.58596 (  195)

*********************** 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
  175 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.232 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8368 (ptm-80) cc_final: 0.8021 (ptp90)
REVERT: 1  137 MET cc_start: 0.8173 (ttm) cc_final: 0.7819 (ttm)
REVERT: 1  153 MET cc_start: 0.7745 (mmm) cc_final: 0.7349 (mmm)
REVERT: 1  197 PHE cc_start: 0.6493 (m-10) cc_final: 0.5885 (m-10)
REVERT: 1  205 MET cc_start: 0.8892 (ttm) cc_final: 0.8605 (mtm)
REVERT: A  133 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7426 (mtm)
REVERT: A  145 GLU cc_start: 0.8170 (mp0) cc_final: 0.7909 (mp0)
REVERT: A  197 PHE cc_start: 0.6449 (m-10) cc_final: 0.5241 (m-10)
REVERT: A  204 MET cc_start: 0.6092 (tmm) cc_final: 0.5874 (tmm)
REVERT: A  211 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.6990 (mt0)
REVERT: A  226 ASP cc_start: 0.7453 (p0) cc_final: 0.7213 (p0)
REVERT: B  100 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7694 (mttp)
REVERT: B  135 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.4860 (pmt170)
REVERT: B  145 GLU cc_start: 0.8393 (mp0) cc_final: 0.8119 (mp0)
REVERT: B  146 ASP cc_start: 0.8319 (t0) cc_final: 0.8073 (t0)
REVERT: B  155 ARG cc_start: 0.7985 (mtt180) cc_final: 0.6333 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8211 (tp30) cc_final: 0.7340 (tm-30)
REVERT: B  207 ARG cc_start: 0.7578 (mtt180) cc_final: 0.5836 (tmm160)
REVERT: B  212 MET cc_start: 0.8500 (tpp) cc_final: 0.8277 (ttm)
REVERT: B  219 LYS cc_start: 0.8117 (mttt) cc_final: 0.6463 (pmtt)
REVERT: B  220 GLU cc_start: 0.8253 (mp0) cc_final: 0.7532 (pp20)
REVERT: C  137 MET cc_start: 0.8077 (ttm) cc_final: 0.7647 (ttm)
REVERT: C  155 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7200 (mtt90)
REVERT: C  195 GLU cc_start: 0.5070 (tm-30) cc_final: 0.4075 (tt0)
REVERT: C  197 PHE cc_start: 0.6401 (m-10) cc_final: 0.6077 (m-10)
REVERT: C  204 MET cc_start: 0.6418 (tmt) cc_final: 0.6095 (tmt)
REVERT: C  220 GLU cc_start: 0.8780 (mp0) cc_final: 0.8173 (mp0)
REVERT: C  226 ASP cc_start: 0.7438 (m-30) cc_final: 0.7115 (t0)
REVERT: D  100 LYS cc_start: 0.7575 (mtmt) cc_final: 0.6633 (mmtt)
REVERT: D  133 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6411 (mpt)
REVERT: D  135 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7240 (tpm170)
REVERT: D  140 PHE cc_start: 0.8286 (m-80) cc_final: 0.6382 (p90)
REVERT: D  143 ASP cc_start: 0.8245 (t0) cc_final: 0.7847 (m-30)
REVERT: D  145 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7991 (mt-10)
REVERT: D  148 TYR cc_start: 0.8258 (p90) cc_final: 0.8027 (p90)
REVERT: D  153 MET cc_start: 0.8616 (mmm) cc_final: 0.6590 (pp-130)
REVERT: D  155 ARG cc_start: 0.8283 (mtt180) cc_final: 0.6712 (ptt90)
REVERT: D  163 ARG cc_start: 0.8790 (mtt180) cc_final: 0.6951 (pmt170)
REVERT: D  204 MET cc_start: 0.6636 (tmm) cc_final: 0.6281 (tmm)
REVERT: D  207 ARG cc_start: 0.8077 (mtt180) cc_final: 0.6012 (mmp-170)
REVERT: D  211 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7855 (mm-40)
REVERT: D  212 MET cc_start: 0.8889 (tpp) cc_final: 0.7001 (pmt)
REVERT: D  221 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8366 (m)
REVERT: D  222 GLN cc_start: 0.8392 (mp-120) cc_final: 0.8021 (mp-120)
REVERT: D  224 TYR cc_start: 0.7849 (m-80) cc_final: 0.7576 (m-80)
REVERT: D  226 ASP cc_start: 0.7757 (p0) cc_final: 0.7361 (p0)
REVERT: D  229 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7113 (pmt170)
  outliers start: 23
  outliers final: 6
  residues processed: 161
  average time/residue: 0.6601
  time to fit residues: 109.7528
Evaluate side-chains
  157 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  211 GLN
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:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    0.1980
   chunk 13 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    3.4386

-------------------------------------------------------------------------------
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**
** 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**
** D 173 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.110898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.095270 restraints weight = 10232.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.94
r_work: 0.3902 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.3816

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= 0.235
  Angle     :  0.677   7.824   7730  Z= 0.364
  Chirality :  0.049   0.143    780
  Planarity :  0.003   0.018   1020
  Dihedral  :  5.675  21.900    780
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 17.65 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG A 229 
 TYR   0.030   0.002   TYR C 217 
 PHE   0.015   0.003   PHE 1 174 
 TRP   0.008   0.001   TRP A 144 
 HIS   0.005   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 5710)
  covalent geometry    : angle       0.67628 ( 7720)
  SS BOND              : bond        0.00121 (    5)
  SS BOND              : angle       0.88585 (   10)
  hydrogen bonds       : bond        0.02956 (   65)
  hydrogen bonds       : angle       4.48823 (  195)

*********************** 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
  178 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.228 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8404 (ptm-80) cc_final: 0.7958 (ptp90)
REVERT: 1  137 MET cc_start: 0.8086 (ttm) cc_final: 0.7547 (ttm)
REVERT: 1  153 MET cc_start: 0.7687 (mmm) cc_final: 0.7343 (mmm)
REVERT: 1  197 PHE cc_start: 0.6197 (m-10) cc_final: 0.5810 (m-10)
REVERT: 1  204 MET cc_start: 0.6158 (tmm) cc_final: 0.5873 (tmm)
REVERT: 1  205 MET cc_start: 0.8809 (ttm) cc_final: 0.8510 (ttm)
REVERT: 1  211 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8302 (mm-40)
REVERT: A  133 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7302 (mtm)
REVERT: A  145 GLU cc_start: 0.8164 (mp0) cc_final: 0.7757 (mp0)
REVERT: A  197 PHE cc_start: 0.6358 (m-10) cc_final: 0.5064 (m-10)
REVERT: A  204 MET cc_start: 0.5970 (tmm) cc_final: 0.5703 (tmm)
REVERT: A  211 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7793 (mt0)
REVERT: B  100 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7700 (mttp)
REVERT: B  135 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.4758 (pmt170)
REVERT: B  145 GLU cc_start: 0.8372 (mp0) cc_final: 0.8136 (mp0)
REVERT: B  146 ASP cc_start: 0.8276 (t0) cc_final: 0.7908 (t0)
REVERT: B  155 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6124 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8168 (tp30) cc_final: 0.7711 (tm-30)
REVERT: B  207 ARG cc_start: 0.7473 (mtt180) cc_final: 0.5724 (tmm160)
REVERT: B  212 MET cc_start: 0.8395 (tpp) cc_final: 0.8128 (ttm)
REVERT: B  219 LYS cc_start: 0.8109 (mttt) cc_final: 0.6449 (pmtt)
REVERT: B  220 GLU cc_start: 0.8177 (mp0) cc_final: 0.7596 (pp20)
REVERT: C  100 LYS cc_start: 0.7570 (mttp) cc_final: 0.7364 (mttp)
REVERT: C  107 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7849 (m-40)
REVERT: C  137 MET cc_start: 0.7975 (ttm) cc_final: 0.7558 (ttm)
REVERT: C  195 GLU cc_start: 0.5106 (tm-30) cc_final: 0.4121 (tt0)
REVERT: C  197 PHE cc_start: 0.6318 (m-10) cc_final: 0.6088 (m-10)
REVERT: C  204 MET cc_start: 0.6300 (tmt) cc_final: 0.5988 (tmt)
REVERT: C  220 GLU cc_start: 0.8758 (mp0) cc_final: 0.8109 (mp0)
REVERT: C  226 ASP cc_start: 0.7412 (m-30) cc_final: 0.7076 (t0)
REVERT: D  100 LYS cc_start: 0.7610 (mtmt) cc_final: 0.6643 (mmtt)
REVERT: D  135 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7072 (tpm170)
REVERT: D  140 PHE cc_start: 0.8345 (m-80) cc_final: 0.6160 (p90)
REVERT: D  143 ASP cc_start: 0.8203 (t0) cc_final: 0.7732 (m-30)
REVERT: D  145 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8008 (mt-10)
REVERT: D  153 MET cc_start: 0.8609 (mmm) cc_final: 0.6521 (pp-130)
REVERT: D  155 ARG cc_start: 0.8210 (mtt180) cc_final: 0.6674 (ptt90)
REVERT: D  163 ARG cc_start: 0.8872 (mtt180) cc_final: 0.6998 (pmt170)
REVERT: D  204 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6159 (tmm)
REVERT: D  207 ARG cc_start: 0.8022 (mtt180) cc_final: 0.5817 (mmp-170)
REVERT: D  212 MET cc_start: 0.8900 (tpp) cc_final: 0.7015 (pmt)
REVERT: D  221 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8343 (m)
REVERT: D  222 GLN cc_start: 0.8277 (mp-120) cc_final: 0.7889 (mp-120)
REVERT: D  226 ASP cc_start: 0.7718 (p0) cc_final: 0.7333 (p0)
REVERT: D  229 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7054 (pmt170)
  outliers start: 24
  outliers final: 5
  residues processed: 163
  average time/residue: 0.7149
  time to fit residues: 119.9753
Evaluate side-chains
  153 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  204 MET
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 61 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 31 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 58 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   overall best weight:    3.8786

-------------------------------------------------------------------------------
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**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** D 173 ASN ** 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 = 0.4111 r_free = 0.4111 target = 0.109826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.093470 restraints weight = 10291.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 2.94
r_work: 0.3856 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   5715  Z= 0.261
  Angle     :  0.715   7.845   7730  Z= 0.384
  Chirality :  0.050   0.168    780
  Planarity :  0.003   0.018   1020
  Dihedral  :  5.818  23.601    780
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.15 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG B 135 
 TYR   0.031   0.003   TYR C 217 
 PHE   0.024   0.003   PHE B 197 
 TRP   0.007   0.001   TRP B  98 
 HIS   0.005   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 5710)
  covalent geometry    : angle       0.71451 ( 7720)
  SS BOND              : bond        0.00142 (    5)
  SS BOND              : angle       0.92933 (   10)
  hydrogen bonds       : bond        0.03083 (   65)
  hydrogen bonds       : angle       4.43964 (  195)

*********************** 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
  166 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.156 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8595 (ptm-80) cc_final: 0.8346 (ptp90)
REVERT: 1  137 MET cc_start: 0.8494 (ttm) cc_final: 0.8198 (ttm)
REVERT: 1  153 MET cc_start: 0.8171 (mmm) cc_final: 0.7873 (mmm)
REVERT: 1  197 PHE cc_start: 0.6544 (m-10) cc_final: 0.6273 (m-10)
REVERT: 1  204 MET cc_start: 0.6776 (tmm) cc_final: 0.6567 (tmt)
REVERT: 1  205 MET cc_start: 0.9024 (ttm) cc_final: 0.8784 (mtm)
REVERT: 1  211 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8726 (mm-40)
REVERT: 1  226 ASP cc_start: 0.8198 (m-30) cc_final: 0.7932 (m-30)
REVERT: A  133 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7739 (mtm)
REVERT: A  145 GLU cc_start: 0.8475 (mp0) cc_final: 0.8223 (mp0)
REVERT: A  197 PHE cc_start: 0.6775 (m-10) cc_final: 0.5735 (m-10)
REVERT: A  210 GLU cc_start: 0.8080 (mp0) cc_final: 0.7773 (mp0)
REVERT: A  211 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8324 (mt0)
REVERT: B  100 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8010 (mttp)
REVERT: B  145 GLU cc_start: 0.8473 (mp0) cc_final: 0.8236 (mp0)
REVERT: B  146 ASP cc_start: 0.8664 (t0) cc_final: 0.8377 (t0)
REVERT: B  155 ARG cc_start: 0.8497 (mtt180) cc_final: 0.6783 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8279 (tp30) cc_final: 0.7891 (tm-30)
REVERT: B  207 ARG cc_start: 0.7740 (mtt180) cc_final: 0.6035 (ttp80)
REVERT: B  212 MET cc_start: 0.8600 (tpp) cc_final: 0.8336 (ttm)
REVERT: B  219 LYS cc_start: 0.8331 (mttt) cc_final: 0.6796 (pmtt)
REVERT: B  220 GLU cc_start: 0.8394 (mp0) cc_final: 0.7621 (pp20)
REVERT: C  107 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8318 (m-40)
REVERT: C  137 MET cc_start: 0.8462 (ttm) cc_final: 0.8116 (ttm)
REVERT: C  204 MET cc_start: 0.6952 (tmt) cc_final: 0.6626 (tmt)
REVERT: C  210 GLU cc_start: 0.7706 (mp0) cc_final: 0.7506 (tm-30)
REVERT: C  211 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8092 (mt0)
REVERT: C  220 GLU cc_start: 0.8928 (mp0) cc_final: 0.8386 (mp0)
REVERT: C  226 ASP cc_start: 0.7692 (m-30) cc_final: 0.7450 (t0)
REVERT: C  229 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6972 (mtp85)
REVERT: D  100 LYS cc_start: 0.7928 (mtmt) cc_final: 0.6990 (mmtt)
REVERT: D  133 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7082 (mpt)
REVERT: D  135 ARG cc_start: 0.8344 (mtt180) cc_final: 0.7567 (tpm170)
REVERT: D  140 PHE cc_start: 0.8259 (m-80) cc_final: 0.6216 (p90)
REVERT: D  143 ASP cc_start: 0.8419 (t0) cc_final: 0.8117 (m-30)
REVERT: D  145 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8327 (mt-10)
REVERT: D  153 MET cc_start: 0.8641 (mmm) cc_final: 0.6655 (pp-130)
REVERT: D  155 ARG cc_start: 0.8527 (mtt180) cc_final: 0.6981 (ptt90)
REVERT: D  163 ARG cc_start: 0.8946 (mtt180) cc_final: 0.7178 (pmt170)
REVERT: D  204 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6724 (tmm)
REVERT: D  207 ARG cc_start: 0.8375 (mtt180) cc_final: 0.6162 (mmp-170)
REVERT: D  212 MET cc_start: 0.8800 (tpp) cc_final: 0.7154 (pmt)
REVERT: D  221 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8741 (m)
REVERT: D  222 GLN cc_start: 0.8808 (mp-120) cc_final: 0.8450 (mp-120)
REVERT: D  226 ASP cc_start: 0.7908 (p0) cc_final: 0.7522 (p0)
REVERT: D  229 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7196 (pmt170)
  outliers start: 22
  outliers final: 5
  residues processed: 151
  average time/residue: 0.7193
  time to fit residues: 111.9086
Evaluate side-chains
  150 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  211 GLN
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain 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  204 MET
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 21 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    2.2786

-------------------------------------------------------------------------------
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**
A 172 ASN
** 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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.112184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.096344 restraints weight = 10206.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 2.88
r_work: 0.3941 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3847 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5715  Z= 0.180
  Angle     :  0.693   7.401   7730  Z= 0.370
  Chirality :  0.049   0.140    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  5.671  23.335    780
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.16 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.81 (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
 ARG   0.004   0.000   ARG A 229 
 TYR   0.031   0.002   TYR C 217 
 PHE   0.021   0.003   PHE C 197 
 TRP   0.007   0.001   TRP B  98 
 HIS   0.004   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 5710)
  covalent geometry    : angle       0.69318 ( 7720)
  SS BOND              : bond        0.00088 (    5)
  SS BOND              : angle       0.83781 (   10)
  hydrogen bonds       : bond        0.02618 (   65)
  hydrogen bonds       : angle       4.36455 (  195)

*********************** 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
  167 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.217 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8367 (ptm-80) cc_final: 0.7890 (ptp90)
REVERT: 1  137 MET cc_start: 0.7978 (ttm) cc_final: 0.7442 (ttm)
REVERT: 1  153 MET cc_start: 0.7575 (mmm) cc_final: 0.7280 (mmm)
REVERT: 1  197 PHE cc_start: 0.6013 (m-10) cc_final: 0.5598 (m-10)
REVERT: 1  204 MET cc_start: 0.6086 (tmm) cc_final: 0.5773 (tmt)
REVERT: 1  205 MET cc_start: 0.8729 (ttm) cc_final: 0.8462 (mtm)
REVERT: 1  211 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8319 (mm-40)
REVERT: A  133 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7140 (mtm)
REVERT: A  145 GLU cc_start: 0.8204 (mp0) cc_final: 0.7781 (mp0)
REVERT: A  197 PHE cc_start: 0.6148 (m-10) cc_final: 0.4982 (m-10)
REVERT: A  211 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7465 (mt0)
REVERT: A  226 ASP cc_start: 0.7217 (p0) cc_final: 0.6912 (p0)
REVERT: A  229 ARG cc_start: 0.7837 (mmt-90) cc_final: 0.7627 (mmt-90)
REVERT: B  135 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5209 (pmt170)
REVERT: B  145 GLU cc_start: 0.8389 (mp0) cc_final: 0.8074 (mp0)
REVERT: B  146 ASP cc_start: 0.8193 (t0) cc_final: 0.7683 (t0)
REVERT: B  155 ARG cc_start: 0.7796 (mtt180) cc_final: 0.6029 (mmp-170)
REVERT: B  206 GLU cc_start: 0.8274 (tp30) cc_final: 0.7522 (tm-30)
REVERT: B  207 ARG cc_start: 0.7486 (mtt180) cc_final: 0.5736 (ttp80)
REVERT: B  212 MET cc_start: 0.8255 (tpp) cc_final: 0.7987 (ttm)
REVERT: B  219 LYS cc_start: 0.8081 (mttt) cc_final: 0.6459 (pmtt)
REVERT: B  220 GLU cc_start: 0.8191 (mp0) cc_final: 0.7548 (pp20)
REVERT: C  107 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7686 (m-40)
REVERT: C  137 MET cc_start: 0.7788 (ttm) cc_final: 0.7424 (ttm)
REVERT: C  195 GLU cc_start: 0.5094 (tm-30) cc_final: 0.4005 (tt0)
REVERT: C  204 MET cc_start: 0.6249 (tmt) cc_final: 0.5971 (tmt)
REVERT: C  220 GLU cc_start: 0.8640 (mp0) cc_final: 0.7989 (mp0)
REVERT: C  226 ASP cc_start: 0.7185 (m-30) cc_final: 0.6761 (t0)
REVERT: C  229 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6799 (mtp85)
REVERT: D  100 LYS cc_start: 0.7701 (mtmt) cc_final: 0.6683 (mmtt)
REVERT: D  133 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6520 (mpt)
REVERT: D  135 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6855 (tpm170)
REVERT: D  140 PHE cc_start: 0.8445 (m-80) cc_final: 0.6155 (p90)
REVERT: D  143 ASP cc_start: 0.8316 (t0) cc_final: 0.7702 (m-30)
REVERT: D  145 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7909 (mt-10)
REVERT: D  153 MET cc_start: 0.8587 (mmm) cc_final: 0.6533 (pp-130)
REVERT: D  155 ARG cc_start: 0.8321 (mtt180) cc_final: 0.6594 (ptt90)
REVERT: D  163 ARG cc_start: 0.8902 (mtt180) cc_final: 0.6858 (pmt170)
REVERT: D  207 ARG cc_start: 0.7998 (mtt180) cc_final: 0.5861 (mmp-170)
REVERT: D  212 MET cc_start: 0.8940 (tpp) cc_final: 0.6996 (pmt)
REVERT: D  221 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8344 (m)
REVERT: D  222 GLN cc_start: 0.8200 (mp-120) cc_final: 0.7820 (mp-120)
REVERT: D  226 ASP cc_start: 0.7653 (p0) cc_final: 0.7280 (p0)
REVERT: D  229 ARG cc_start: 0.8290 (mtt180) cc_final: 0.6942 (pmt170)
  outliers start: 21
  outliers final: 5
  residues processed: 154
  average time/residue: 0.6584
  time to fit residues: 104.6371
Evaluate side-chains
  156 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain B residue  135 ARG
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain 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  221 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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**
A 172 ASN
** 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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.111053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.094805 restraints weight = 10141.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.91
r_work: 0.3822 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5715  Z= 0.214
  Angle     :  0.719   8.023   7730  Z= 0.383
  Chirality :  0.050   0.144    780
  Planarity :  0.003   0.020   1020
  Dihedral  :  5.735  24.227    780
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.00 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.84 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG 1 207 
 TYR   0.031   0.002   TYR C 217 
 PHE   0.027   0.003   PHE B 197 
 TRP   0.007   0.001   TRP B  98 
 HIS   0.004   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 5710)
  covalent geometry    : angle       0.71828 ( 7720)
  SS BOND              : bond        0.00137 (    5)
  SS BOND              : angle       0.98869 (   10)
  hydrogen bonds       : bond        0.02723 (   65)
  hydrogen bonds       : angle       4.40945 (  195)

*********************** 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
  164 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.157 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.8018 (ptp90)
REVERT: 1  137 MET cc_start: 0.8137 (ttm) cc_final: 0.7745 (ttm)
REVERT: 1  153 MET cc_start: 0.7790 (mmm) cc_final: 0.7485 (mmm)
REVERT: 1  197 PHE cc_start: 0.6175 (m-10) cc_final: 0.5832 (m-10)
REVERT: 1  204 MET cc_start: 0.6343 (tmm) cc_final: 0.6128 (tmt)
REVERT: A  133 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7339 (mtm)
REVERT: A  145 GLU cc_start: 0.8324 (mp0) cc_final: 0.7915 (mp0)
REVERT: A  197 PHE cc_start: 0.6415 (m-10) cc_final: 0.5367 (m-10)
REVERT: A  211 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7129 (mt0)
REVERT: A  229 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7736 (mmt-90)
REVERT: B  145 GLU cc_start: 0.8427 (mp0) cc_final: 0.8129 (mp0)
REVERT: B  146 ASP cc_start: 0.8334 (t0) cc_final: 0.7866 (t0)
REVERT: B  155 ARG cc_start: 0.8011 (mtt180) cc_final: 0.6247 (mmp-170)
REVERT: B  206 GLU cc_start: 0.7882 (tp30) cc_final: 0.7600 (tm-30)
REVERT: B  207 ARG cc_start: 0.7544 (mtt180) cc_final: 0.5766 (tmm160)
REVERT: B  212 MET cc_start: 0.8437 (tpp) cc_final: 0.8141 (ttm)
REVERT: B  219 LYS cc_start: 0.8162 (mttt) cc_final: 0.6552 (pmtt)
REVERT: B  220 GLU cc_start: 0.8278 (mp0) cc_final: 0.7560 (pp20)
REVERT: C  107 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7979 (m-40)
REVERT: C  137 MET cc_start: 0.8046 (ttm) cc_final: 0.7638 (ttm)
REVERT: C  195 GLU cc_start: 0.5173 (tm-30) cc_final: 0.4202 (tt0)
REVERT: C  204 MET cc_start: 0.6504 (tmt) cc_final: 0.6146 (tmt)
REVERT: C  220 GLU cc_start: 0.8773 (mp0) cc_final: 0.8113 (mp0)
REVERT: C  226 ASP cc_start: 0.7328 (m-30) cc_final: 0.6923 (t0)
REVERT: C  229 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6928 (mtp85)
REVERT: D  100 LYS cc_start: 0.7761 (mtmt) cc_final: 0.6738 (mmtt)
REVERT: D  133 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6702 (mpt)
REVERT: D  135 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7106 (tpm170)
REVERT: D  140 PHE cc_start: 0.8401 (m-80) cc_final: 0.6111 (p90)
REVERT: D  143 ASP cc_start: 0.8370 (t0) cc_final: 0.7851 (m-30)
REVERT: D  145 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7931 (mt-10)
REVERT: D  153 MET cc_start: 0.8574 (mmm) cc_final: 0.6517 (pp-130)
REVERT: D  155 ARG cc_start: 0.8347 (mtt180) cc_final: 0.6720 (ptt90)
REVERT: D  163 ARG cc_start: 0.9003 (mtt180) cc_final: 0.7001 (pmt170)
REVERT: D  207 ARG cc_start: 0.8132 (mtt180) cc_final: 0.5939 (mmp-170)
REVERT: D  212 MET cc_start: 0.8823 (tpp) cc_final: 0.6942 (pmt)
REVERT: D  221 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8507 (m)
REVERT: D  222 GLN cc_start: 0.8390 (mp-120) cc_final: 0.7993 (mp-120)
REVERT: D  226 ASP cc_start: 0.7831 (p0) cc_final: 0.7437 (p0)
REVERT: D  229 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7068 (pmt170)
  outliers start: 22
  outliers final: 7
  residues processed: 151
  average time/residue: 0.6993
  time to fit residues: 108.8193
Evaluate side-chains
  152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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**
** 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 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** D 173 ASN ** 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 = 0.4170 r_free = 0.4170 target = 0.113571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.097052 restraints weight = 10048.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 3.03
r_work: 0.3922 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5715  Z= 0.149
  Angle     :  0.726   8.230   7730  Z= 0.387
  Chirality :  0.050   0.205    780
  Planarity :  0.003   0.027   1020
  Dihedral  :  5.575  24.393    780
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.84 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 147 
 TYR   0.032   0.002   TYR C 217 
 PHE   0.022   0.003   PHE C 197 
 TRP   0.007   0.001   TRP B  98 
 HIS   0.003   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5710)
  covalent geometry    : angle       0.72564 ( 7720)
  SS BOND              : bond        0.00093 (    5)
  SS BOND              : angle       0.69043 (   10)
  hydrogen bonds       : bond        0.02212 (   65)
  hydrogen bonds       : angle       4.37462 (  195)

*********************** 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
  158 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.186 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.7872 (ptp90)
REVERT: 1  137 MET cc_start: 0.7825 (ttm) cc_final: 0.7445 (ttm)
REVERT: 1  153 MET cc_start: 0.7581 (mmm) cc_final: 0.7280 (mmm)
REVERT: 1  197 PHE cc_start: 0.6050 (m-10) cc_final: 0.5758 (m-10)
REVERT: 1  204 MET cc_start: 0.5984 (tmm) cc_final: 0.5669 (tmt)
REVERT: 1  211 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8167 (mm-40)
REVERT: A  133 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7095 (mtm)
REVERT: A  145 GLU cc_start: 0.8162 (mp0) cc_final: 0.7749 (mp0)
REVERT: A  197 PHE cc_start: 0.6281 (m-10) cc_final: 0.5414 (m-10)
REVERT: A  211 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7601 (mt0)
REVERT: A  229 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7610 (mmt-90)
REVERT: B  145 GLU cc_start: 0.8292 (mp0) cc_final: 0.7965 (mp0)
REVERT: B  146 ASP cc_start: 0.8074 (t0) cc_final: 0.7600 (t0)
REVERT: B  155 ARG cc_start: 0.7681 (mtt180) cc_final: 0.5966 (mmp-170)
REVERT: B  175 VAL cc_start: 0.8663 (t) cc_final: 0.8229 (m)
REVERT: B  207 ARG cc_start: 0.7346 (mtt180) cc_final: 0.5654 (tmm160)
REVERT: B  212 MET cc_start: 0.8245 (tpp) cc_final: 0.8014 (ttm)
REVERT: B  219 LYS cc_start: 0.8015 (mttt) cc_final: 0.6449 (pmtt)
REVERT: B  220 GLU cc_start: 0.8224 (mp0) cc_final: 0.7543 (pp20)
REVERT: C  107 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7727 (m-40)
REVERT: C  137 MET cc_start: 0.7712 (ttm) cc_final: 0.7334 (ttm)
REVERT: C  146 ASP cc_start: 0.7956 (t0) cc_final: 0.7741 (t0)
REVERT: C  147 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7784 (ptp-170)
REVERT: C  195 GLU cc_start: 0.4939 (tm-30) cc_final: 0.4202 (tt0)
REVERT: C  197 PHE cc_start: 0.5870 (m-10) cc_final: 0.5066 (m-10)
REVERT: C  204 MET cc_start: 0.6171 (tmt) cc_final: 0.5921 (tmt)
REVERT: C  220 GLU cc_start: 0.8667 (mp0) cc_final: 0.7995 (mp0)
REVERT: C  226 ASP cc_start: 0.7162 (m-30) cc_final: 0.6751 (t0)
REVERT: C  229 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6745 (mtp85)
REVERT: D  100 LYS cc_start: 0.7585 (mtmt) cc_final: 0.6585 (mmtt)
REVERT: D  135 ARG cc_start: 0.7794 (mtt180) cc_final: 0.6919 (tpm170)
REVERT: D  140 PHE cc_start: 0.8403 (m-80) cc_final: 0.6087 (p90)
REVERT: D  143 ASP cc_start: 0.8210 (t0) cc_final: 0.7579 (m-30)
REVERT: D  145 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7759 (mt-10)
REVERT: D  148 TYR cc_start: 0.8282 (p90) cc_final: 0.8040 (p90)
REVERT: D  153 MET cc_start: 0.8598 (mmm) cc_final: 0.6483 (pp-130)
REVERT: D  155 ARG cc_start: 0.8221 (mtt180) cc_final: 0.6572 (ptt90)
REVERT: D  163 ARG cc_start: 0.8903 (mtt180) cc_final: 0.6888 (pmt-80)
REVERT: D  207 ARG cc_start: 0.7997 (mtt180) cc_final: 0.5754 (mmp-170)
REVERT: D  212 MET cc_start: 0.8806 (tpp) cc_final: 0.6901 (pmt)
REVERT: D  221 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8327 (m)
REVERT: D  222 GLN cc_start: 0.8187 (mp-120) cc_final: 0.7800 (mp-120)
REVERT: D  226 ASP cc_start: 0.7641 (p0) cc_final: 0.7213 (p0)
REVERT: D  229 ARG cc_start: 0.8270 (mtt180) cc_final: 0.6964 (pmt170)
  outliers start: 16
  outliers final: 4
  residues processed: 148
  average time/residue: 0.7301
  time to fit residues: 111.2206
Evaluate side-chains
  147 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  229 ARG
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 GLN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 GLN
** D 173 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.111807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.095626 restraints weight = 10284.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.93
r_work: 0.3852 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5715  Z= 0.240
  Angle     :  0.801   8.887   7730  Z= 0.425
  Chirality :  0.051   0.198    780
  Planarity :  0.003   0.025   1020
  Dihedral  :  5.839  24.965    780
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.85 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.88 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 135 
 TYR   0.032   0.002   TYR C 217 
 PHE   0.025   0.003   PHE B 197 
 TRP   0.006   0.001   TRP B  98 
 HIS   0.005   0.001   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 5710)
  covalent geometry    : angle       0.80055 ( 7720)
  SS BOND              : bond        0.00092 (    5)
  SS BOND              : angle       0.90443 (   10)
  hydrogen bonds       : bond        0.02800 (   65)
  hydrogen bonds       : angle       4.38843 (  195)

********************** 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
  156 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.153 
Fit side-chains
REVERT: 1  135 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8133 (ptp90)
REVERT: 1  137 MET cc_start: 0.8285 (ttm) cc_final: 0.7948 (ttm)
REVERT: 1  153 MET cc_start: 0.7879 (mmm) cc_final: 0.7594 (mmm)
REVERT: 1  197 PHE cc_start: 0.6369 (m-10) cc_final: 0.6052 (m-10)
REVERT: 1  204 MET cc_start: 0.6456 (tmm) cc_final: 0.6135 (tmt)
REVERT: 1  211 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8663 (mm-40)
REVERT: A  133 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7436 (mtm)
REVERT: A  145 GLU cc_start: 0.8389 (mp0) cc_final: 0.7981 (mp0)
REVERT: A  197 PHE cc_start: 0.6356 (m-10) cc_final: 0.5475 (m-10)
REVERT: A  211 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.7913 (mt0)
REVERT: A  229 ARG cc_start: 0.8102 (mmt-90) cc_final: 0.7808 (mmt-90)
REVERT: B  145 GLU cc_start: 0.8467 (mp0) cc_final: 0.8170 (mp0)
REVERT: B  146 ASP cc_start: 0.8420 (t0) cc_final: 0.7974 (t0)
REVERT: B  155 ARG cc_start: 0.8132 (mtt180) cc_final: 0.6369 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: B  207 ARG cc_start: 0.7866 (mtt180) cc_final: 0.5905 (tmm160)
REVERT: B  219 LYS cc_start: 0.8196 (mttt) cc_final: 0.6595 (pmtt)
REVERT: B  220 GLU cc_start: 0.8304 (mp0) cc_final: 0.7591 (pp20)
REVERT: C  107 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8125 (m-40)
REVERT: C  137 MET cc_start: 0.8227 (ttm) cc_final: 0.7820 (ttm)
REVERT: C  195 GLU cc_start: 0.5272 (tm-30) cc_final: 0.4086 (tt0)
REVERT: C  204 MET cc_start: 0.6611 (tmt) cc_final: 0.6319 (tmt)
REVERT: C  220 GLU cc_start: 0.8839 (mp0) cc_final: 0.8220 (mp0)
REVERT: C  226 ASP cc_start: 0.7397 (m-30) cc_final: 0.7007 (t0)
REVERT: C  229 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7015 (mtp85)
REVERT: D  100 LYS cc_start: 0.7884 (mtmt) cc_final: 0.6872 (mmtt)
REVERT: D  135 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7258 (tpm170)
REVERT: D  140 PHE cc_start: 0.8369 (m-80) cc_final: 0.6052 (p90)
REVERT: D  143 ASP cc_start: 0.8423 (t0) cc_final: 0.7981 (m-30)
REVERT: D  145 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7988 (mt-10)
REVERT: D  153 MET cc_start: 0.8571 (mmm) cc_final: 0.6540 (pp-130)
REVERT: D  155 ARG cc_start: 0.8376 (mtt180) cc_final: 0.6820 (ptt90)
REVERT: D  163 ARG cc_start: 0.9000 (mtt180) cc_final: 0.7086 (pmt170)
REVERT: D  167 GLN cc_start: 0.8669 (tt0) cc_final: 0.8401 (tt0)
REVERT: D  207 ARG cc_start: 0.8295 (mtt180) cc_final: 0.6020 (mmp-170)
REVERT: D  212 MET cc_start: 0.8814 (tpp) cc_final: 0.7016 (pmt)
REVERT: D  221 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8627 (m)
REVERT: D  226 ASP cc_start: 0.7868 (p0) cc_final: 0.7440 (p0)
REVERT: D  229 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7076 (pmt170)
  outliers start: 18
  outliers final: 6
  residues processed: 149
  average time/residue: 0.6863
  time to fit residues: 105.3292
Evaluate side-chains
  149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  140 PHE
Chi-restraints excluded: chain 1 residue  211 GLN
Chi-restraints excluded: chain 1 residue  221 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  211 GLN
Chi-restraints excluded: chain 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  145 GLU
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  221 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 63 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    5.9788

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.107873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.091518 restraints weight = 10351.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.91
r_work: 0.3838 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.4480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.047   5715  Z= 0.390
  Angle     :  0.902   9.384   7730  Z= 0.484
  Chirality :  0.054   0.222    780
  Planarity :  0.004   0.025   1020
  Dihedral  :  6.326  25.392    780
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.52 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.00 (0.25), residues: 680
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.19), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 135 
 TYR   0.033   0.003   TYR C 217 
 PHE   0.017   0.003   PHE 1 174 
 TRP   0.008   0.001   TRP B  98 
 HIS   0.007   0.002   HIS 1 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00876 ( 5710)
  covalent geometry    : angle       0.90163 ( 7720)
  SS BOND              : bond        0.00264 (    5)
  SS BOND              : angle       1.17042 (   10)
  hydrogen bonds       : bond        0.03620 (   65)
  hydrogen bonds       : angle       4.56710 (  195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2327.38 seconds
wall clock time: 40 minutes 17.47 seconds (2417.47 seconds total)