Starting phenix.real_space_refine
on Wed Jul 23 15:28:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u13_26276/07_2025/7u13_26276.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u13_26276/07_2025/7u13_26276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2025/7u13_26276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2025/7u13_26276.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2025/7u13_26276.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2025/7u13_26276.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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      21      5.16       5
     C    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 4.43, per 1000 atoms: 1.28
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (97.734, 117.066, 31.146, 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      21     16.00
     O     702      8.00
     N     531      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " 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
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 767.2 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 68.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131
      removed outlier: 6.322A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131
      removed outlier: 6.322A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   SER B 130 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA C 131 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TYR B 132 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 177
      removed outlier: 9.050A  pdb=" N   THR A 141 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   LEU B 144 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   TYR A 143 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 9.078A  pdb=" N   ILE B 146 " --> pdb=" O   TYR A 143 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ASN A 145 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   ASN B 148 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   THR A 147 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   LEU B 150 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   THR A 149 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   ILE B 152 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ASN A 151 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ASN B 154 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR A 153 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ASN B 156 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASN A 155 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   TYR B 158 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TYR A 157 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   VAL B 160 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   SER A 159 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   VAL B 162 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   GLU A 161 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 9.930A  pdb=" N   ASN B 164 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 9.474A  pdb=" N   GLU A 163 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 10.042A  pdb=" N   THR B 166 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ILE A 165 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   GLN B 168 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ALA A 167 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   GLN B 170 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   VAL A 169 " --> pdb=" O   GLN B 170 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   SER B 172 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   PHE A 171 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 8.292A  pdb=" N   THR B 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LYS A 173 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   ILE B 176 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL A 175 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 9.093A  pdb=" N   THR B 141 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 9.071A  pdb=" N   LEU C 144 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   TYR B 143 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   ILE C 146 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ASN B 145 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ASN C 148 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR B 147 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   LEU C 150 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   THR B 149 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ILE C 152 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ASN B 151 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ASN C 154 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   THR B 153 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   ASN C 156 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ASN B 155 " --> pdb=" O   ASN C 156 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   TYR C 158 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TYR B 157 " --> pdb=" O   TYR C 158 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   VAL C 160 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   SER B 159 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL C 162 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   GLU B 161 " --> pdb=" O   VAL C 162 " (cutoff:3.500A)
      removed outlier: 9.877A  pdb=" N   ASN C 164 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 9.408A  pdb=" N   GLU B 163 " --> pdb=" O   ASN C 164 " (cutoff:3.500A)
      removed outlier: 9.975A  pdb=" N   THR C 166 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE B 165 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   GLN C 168 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ALA B 167 " --> pdb=" O   GLN C 168 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLN C 170 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   VAL B 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   SER C 172 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE B 171 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   THR C 174 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LYS B 173 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   ILE C 176 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL B 175 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.630A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.458A  pdb=" N   THR A 185 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   THR B 185 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 8.929A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 9.771A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   TYR B 197 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP A 196 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 9.784A  pdb=" N   ILE C 195 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   GLN B 194 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   TYR C 197 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B 196 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203
      removed outlier: 6.278A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   VAL B 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219
      removed outlier: 6.960A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   PHE C 213 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 228
      removed outlier: 6.853A  pdb=" N   ASN B 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ASN C 223 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.470A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 249 through 253
      removed outlier: 6.871A  pdb=" N   TYR B 250 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   TYR C 250 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)

    53 hydrogen bonds defined for protein.
    156 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: 0.85

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.06 -     1.21: 9
        1.21 -     1.36: 1059
        1.36 -     1.51: 1090
        1.51 -     1.66: 1322
        1.66 -     1.81: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" CG  PRO C 189 "
       pdb=" CD  PRO C 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.173  0.330 3.40e-02 8.65e+02 9.43e+01
  bond pdb=" CG  PRO B 189 "
       pdb=" CD  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.173  0.330 3.40e-02 8.65e+02 9.40e+01
  bond pdb=" CG  PRO A 189 "
       pdb=" CD  PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.174  0.329 3.40e-02 8.65e+02 9.35e+01
  bond pdb=" CB  PRO A 189 "
       pdb=" CG  PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.063  0.429 5.00e-02 4.00e+02 7.38e+01
  bond pdb=" CB  PRO B 189 "
       pdb=" CG  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.063  0.429 5.00e-02 4.00e+02 7.38e+01
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.77: 4779
       14.77 -    29.54: 3
       29.54 -    44.31: 3
       44.31 -    59.08: 0
       59.08 -    73.86: 3
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" CB  PRO A 189 "
        pdb=" CG  PRO A 189 "
        pdb=" CD  PRO A 189 "
      ideal   model   delta    sigma   weight residual
     106.10  179.96  -73.86 3.20e+00 9.77e-02 5.33e+02
  angle pdb=" CB  PRO B 189 "
        pdb=" CG  PRO B 189 "
        pdb=" CD  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     106.10  179.92  -73.82 3.20e+00 9.77e-02 5.32e+02
  angle pdb=" CB  PRO C 189 "
        pdb=" CG  PRO C 189 "
        pdb=" CD  PRO C 189 "
      ideal   model   delta    sigma   weight residual
     106.10  179.89  -73.79 3.20e+00 9.77e-02 5.32e+02
  angle pdb=" N   PRO A 189 "
        pdb=" CD  PRO A 189 "
        pdb=" CG  PRO A 189 "
      ideal   model   delta    sigma   weight residual
     103.20   73.84   29.36 1.50e+00 4.44e-01 3.83e+02
  angle pdb=" N   PRO C 189 "
        pdb=" CD  PRO C 189 "
        pdb=" CG  PRO C 189 "
      ideal   model   delta    sigma   weight residual
     103.20   73.95   29.25 1.50e+00 4.44e-01 3.80e+02
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.07: 2068
       26.07 -    52.13: 171
       52.13 -    78.20: 18
       78.20 -   104.27: 10
      104.27 -   130.33: 4
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" N   PRO A 189 "
           pdb=" CG  PRO A 189 "
           pdb=" CD  PRO A 189 "
           pdb=" CB  PRO A 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -160.33  130.33     1      1.50e+01 4.44e-03 7.03e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.46   59.54     1      1.00e+01 1.00e-02 4.73e+01
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.48   59.52     1      1.00e+01 1.00e-02 4.73e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 438
       0.072 -    0.143: 139
       0.143 -    0.215: 26
       0.215 -    0.286: 0
       0.286 -    0.358: 3
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CB  ILE C 203 "
            pdb=" CA  ILE C 203 "
            pdb=" CG1 ILE C 203 "
            pdb=" CG2 ILE C 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" CB  ILE A 203 "
            pdb=" CA  ILE A 203 "
            pdb=" CG1 ILE A 203 "
            pdb=" CG2 ILE A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CB  ILE B 203 "
            pdb=" CA  ILE B 203 "
            pdb=" CG1 ILE B 203 "
            pdb=" CG2 ILE B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.16e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 157 "    0.008 2.00e-02 2.50e+03   1.44e-02 4.15e+00
        pdb=" CG  TYR A 157 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 157 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 157 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 157 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 157 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 157 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 157 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 157 "    0.009 2.00e-02 2.50e+03   1.43e-02 4.11e+00
        pdb=" CG  TYR B 157 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 157 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 157 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 157 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 157 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 157 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 157 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 157 "    0.009 2.00e-02 2.50e+03   1.43e-02 4.09e+00
        pdb=" CG  TYR C 157 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 157 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 157 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 157 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 157 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 157 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 157 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 82
        2.68 -     3.23: 3267
        3.23 -     3.79: 5409
        3.79 -     4.34: 6959
        4.34 -     4.90: 12721
  Nonbonded interactions: 28438
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 197 "
            pdb=" NZ  LYS B 220 "
     model   vdw
     2.120 3.120
  nonbonded pdb=" NE2 GLN C 229 "
            pdb=" OG1 THR C 234 "
     model   vdw
     2.139 3.120
  nonbonded pdb=" NE2 GLN B 229 "
            pdb=" OG1 THR B 234 "
     model   vdw
     2.139 3.120
  nonbonded pdb=" NE2 GLN A 229 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" OH  TYR B 197 "
            pdb=" NZ  LYS C 220 "
     model   vdw
     2.168 3.120
  ... (remaining 28433 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 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
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:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     15.410
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4696
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      :  0.018   0.429   3531  Z= 0.536
  Angle     :  2.429  73.856   4830  Z= 1.081
  Chirality :  0.071   0.358    606
  Planarity :  0.006   0.049    579
  Dihedral  : 19.232 130.333   1476
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 29.95
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  : 11.28 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  :  3.15 %
    Favored  : 90.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS A 222 
 PHE   0.016   0.004   PHE A 171 
 TYR   0.033   0.005   TYR A 157 
 ARG   0.004   0.001   ARG C 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00487 (   12)
  link_NAG-ASN         : angle       1.98188 (   36)
  hydrogen bonds       : bond        0.12713 (   53)
  hydrogen bonds       : angle       8.17157 (  156)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       3.45170 (    6)
  covalent geometry    : bond        0.01758 ( 3516)
  covalent geometry    : angle       2.43083 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.4399 (mmm) cc_final: 0.3481 (ptt)
REVERT: B  231 THR cc_start: 0.6681 (p) cc_final: 0.6419 (p)
REVERT: C  219 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5797 (mm)
  outliers start: 24
  outliers final: 9
  residues processed: 136
  average time/residue: 0.9081
  time to fit residues: 127.9340
Evaluate side-chains
  75 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  219 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0870
   chunk 16 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    3.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
B 229 GLN
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 170 GLN
** C 242 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 = 0.5719 r_free = 0.5719 target = 0.331478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.6036 r_free = 0.6036 target = 0.294894 restraints weight = 31110.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.5610 rms_B_bonded: 5.48
r_work: 0.5939 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.5939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5596 r_free = 0.5596    target_work(ls_wunit_k1) = 0.315         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5594 r_free = 0.5594    target_work(ls_wunit_k1) = 0.314         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5323
moved from start:          0.6777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3531  Z= 0.232
  Angle     :  0.991   9.893   4830  Z= 0.507
  Chirality :  0.061   0.263    606
  Planarity :  0.006   0.062    579
  Dihedral  : 15.719 107.772    729
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  7.87 %
    Allowed  : 17.06 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.004   HIS A 239 
 PHE   0.011   0.002   PHE A 237 
 TYR   0.020   0.003   TYR C 248 
 ARG   0.002   0.001   ARG A 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00724 (   12)
  link_NAG-ASN         : angle       2.90711 (   36)
  hydrogen bonds       : bond        0.04418 (   53)
  hydrogen bonds       : angle       6.67700 (  156)
  SS BOND              : bond        0.00790 (    3)
  SS BOND              : angle       2.35375 (    6)
  covalent geometry    : bond        0.00523 ( 3516)
  covalent geometry    : angle       0.95891 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.4552 (mmm) cc_final: 0.2112 (ptt)
REVERT: A  236 TYR cc_start: 0.5124 (p90) cc_final: 0.3637 (t80)
REVERT: A  245 GLN cc_start: 0.6743 (mp10) cc_final: 0.6446 (tt0)
REVERT: B  231 THR cc_start: 0.6391 (p) cc_final: 0.6137 (p)
REVERT: C  125 TYR cc_start: 0.4929 (t80) cc_final: 0.3374 (p90)
REVERT: C  126 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5498 (mm)
REVERT: C  216 LEU cc_start: 0.7673 (mm) cc_final: 0.7350 (tt)
REVERT: C  250 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4661 (p90)
  outliers start: 30
  outliers final: 7
  residues processed: 103
  average time/residue: 0.8417
  time to fit residues: 90.3811
Evaluate side-chains
  85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  220 LYS
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5698 r_free = 0.5698 target = 0.326577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5979 r_free = 0.5979 target = 0.288615 restraints weight = 18799.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.5575 rms_B_bonded: 4.35
r_work: 0.5933 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.5895 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.5895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5528 r_free = 0.5528    target_work(ls_wunit_k1) = 0.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5528 r_free = 0.5528    target_work(ls_wunit_k1) = 0.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5426
moved from start:          0.7807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3531  Z= 0.194
  Angle     :  0.949  11.147   4830  Z= 0.485
  Chirality :  0.058   0.280    606
  Planarity :  0.004   0.036    579
  Dihedral  : 14.129 105.835    713
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 26.77 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS C 239 
 PHE   0.013   0.002   PHE B 171 
 TYR   0.017   0.002   TYR A 125 
 ARG   0.001   0.000   ARG B 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00560 (   12)
  link_NAG-ASN         : angle       2.52622 (   36)
  hydrogen bonds       : bond        0.04404 (   53)
  hydrogen bonds       : angle       6.24846 (  156)
  SS BOND              : bond        0.00742 (    3)
  SS BOND              : angle       2.11401 (    6)
  covalent geometry    : bond        0.00440 ( 3516)
  covalent geometry    : angle       0.92458 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.4851 (mmm) cc_final: 0.2497 (ptt)
REVERT: A  219 ILE cc_start: 0.4407 (OUTLIER) cc_final: 0.4067 (pp)
REVERT: A  245 GLN cc_start: 0.6613 (mp10) cc_final: 0.6201 (tt0)
REVERT: B  249 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.6131 (tt0)
REVERT: C  216 LEU cc_start: 0.7417 (mm) cc_final: 0.7021 (tt)
REVERT: C  250 TYR cc_start: 0.5577 (OUTLIER) cc_final: 0.4901 (p90)
  outliers start: 25
  outliers final: 11
  residues processed: 101
  average time/residue: 0.8231
  time to fit residues: 86.4279
Evaluate side-chains
  92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  249 GLN
Chi-restraints excluded: chain C residue  132 TYR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5646 r_free = 0.5646 target = 0.314195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5960 r_free = 0.5960 target = 0.277212 restraints weight = 20013.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.5553 rms_B_bonded: 3.91
r_work: 0.5919 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.5880 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.5880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5510 r_free = 0.5510    target_work(ls_wunit_k1) = 0.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5510 r_free = 0.5510    target_work(ls_wunit_k1) = 0.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5649
moved from start:          0.9685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   3531  Z= 0.283
  Angle     :  1.127  11.347   4830  Z= 0.571
  Chirality :  0.066   0.344    606
  Planarity :  0.005   0.031    579
  Dihedral  : 14.626 104.763    711
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 29.40 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.31), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 239 
 PHE   0.025   0.003   PHE B 237 
 TYR   0.020   0.003   TYR A 250 
 ARG   0.002   0.000   ARG A 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00782 (   12)
  link_NAG-ASN         : angle       3.69118 (   36)
  hydrogen bonds       : bond        0.05464 (   53)
  hydrogen bonds       : angle       6.59939 (  156)
  SS BOND              : bond        0.01278 (    3)
  SS BOND              : angle       2.96734 (    6)
  covalent geometry    : bond        0.00642 ( 3516)
  covalent geometry    : angle       1.08050 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  207 MET cc_start: 0.1732 (tpt) cc_final: 0.0718 (tpt)
REVERT: A  219 ILE cc_start: 0.4558 (OUTLIER) cc_final: 0.4348 (pp)
REVERT: B  219 ILE cc_start: 0.6341 (mm) cc_final: 0.6134 (pt)
  outliers start: 27
  outliers final: 11
  residues processed: 93
  average time/residue: 0.8279
  time to fit residues: 80.1082
Evaluate side-chains
  81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0370
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    5.0066

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
C 249 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5605 r_free = 0.5605 target = 0.312290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5957 r_free = 0.5957 target = 0.276101 restraints weight = 26211.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.5517 rms_B_bonded: 4.44
r_work: 0.5875 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.5834 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.5834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5454 r_free = 0.5454    target_work(ls_wunit_k1) = 0.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5454 r_free = 0.5454    target_work(ls_wunit_k1) = 0.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5681
moved from start:          1.0430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   3531  Z= 0.250
  Angle     :  1.060  10.125   4830  Z= 0.535
  Chirality :  0.063   0.317    606
  Planarity :  0.004   0.029    579
  Dihedral  : 14.337 103.089    711
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 30.71 %
    Favored  : 61.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.31), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.23), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 239 
 PHE   0.019   0.003   PHE B 237 
 TYR   0.019   0.003   TYR C 125 
 ARG   0.002   0.000   ARG C 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00594 (   12)
  link_NAG-ASN         : angle       3.59582 (   36)
  hydrogen bonds       : bond        0.05075 (   53)
  hydrogen bonds       : angle       6.81835 (  156)
  SS BOND              : bond        0.01631 (    3)
  SS BOND              : angle       1.99004 (    6)
  covalent geometry    : bond        0.00565 ( 3516)
  covalent geometry    : angle       1.01521 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  219 ILE cc_start: 0.4657 (OUTLIER) cc_final: 0.4185 (pp)
REVERT: B  163 GLU cc_start: 0.5837 (mp0) cc_final: 0.5152 (mp0)
REVERT: C  140 ARG cc_start: 0.4457 (OUTLIER) cc_final: 0.3779 (ppt90)
REVERT: C  163 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5628 (mp0)
  outliers start: 28
  outliers final: 13
  residues processed: 89
  average time/residue: 0.7922
  time to fit residues: 73.4330
Evaluate side-chains
  86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  163 GLU
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5658 r_free = 0.5658 target = 0.318250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.6033 r_free = 0.6033 target = 0.283300 restraints weight = 31779.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.5563 rms_B_bonded: 5.05
r_work: 0.5915 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.5915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5540 r_free = 0.5540    target_work(ls_wunit_k1) = 0.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5540 r_free = 0.5540    target_work(ls_wunit_k1) = 0.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5522
moved from start:          1.0509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3531  Z= 0.171
  Angle     :  0.956  11.531   4830  Z= 0.475
  Chirality :  0.058   0.247    606
  Planarity :  0.003   0.025    579
  Dihedral  : 13.427 101.768    711
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 32.02 %
    Favored  : 62.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.07 (0.31), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS A 239 
 PHE   0.024   0.002   PHE C 237 
 TYR   0.015   0.002   TYR A 125 
 ARG   0.001   0.000   ARG C 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (   12)
  link_NAG-ASN         : angle       3.04198 (   36)
  hydrogen bonds       : bond        0.04551 (   53)
  hydrogen bonds       : angle       6.65611 (  156)
  SS BOND              : bond        0.00817 (    3)
  SS BOND              : angle       0.87905 (    6)
  covalent geometry    : bond        0.00378 ( 3516)
  covalent geometry    : angle       0.92252 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  219 ILE cc_start: 0.4165 (OUTLIER) cc_final: 0.3738 (pp)
REVERT: C  132 TYR cc_start: 0.3035 (OUTLIER) cc_final: 0.2768 (t80)
REVERT: C  250 TYR cc_start: 0.5839 (OUTLIER) cc_final: 0.5203 (p90)
  outliers start: 22
  outliers final: 11
  residues processed: 88
  average time/residue: 0.8479
  time to fit residues: 77.6916
Evaluate side-chains
  79 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  132 TYR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 22 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:   20.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5625 r_free = 0.5625 target = 0.314441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5968 r_free = 0.5968 target = 0.278647 restraints weight = 24880.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.5533 rms_B_bonded: 4.40
r_work: 0.5892 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.5841 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.5841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5466 r_free = 0.5466    target_work(ls_wunit_k1) = 0.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5466 r_free = 0.5466    target_work(ls_wunit_k1) = 0.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5648
moved from start:          1.0886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3531  Z= 0.207
  Angle     :  1.018   9.958   4830  Z= 0.506
  Chirality :  0.060   0.260    606
  Planarity :  0.004   0.025    579
  Dihedral  : 13.241  98.784    711
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 32.81 %
    Favored  : 60.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.31), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 239 
 PHE   0.018   0.002   PHE A 237 
 TYR   0.016   0.003   TYR C 125 
 ARG   0.001   0.000   ARG C 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00428 (   12)
  link_NAG-ASN         : angle       3.19420 (   36)
  hydrogen bonds       : bond        0.04529 (   53)
  hydrogen bonds       : angle       6.50591 (  156)
  SS BOND              : bond        0.00934 (    3)
  SS BOND              : angle       2.08139 (    6)
  covalent geometry    : bond        0.00474 ( 3516)
  covalent geometry    : angle       0.98149 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  184 ILE cc_start: 0.4089 (OUTLIER) cc_final: 0.3579 (pp)
REVERT: A  207 MET cc_start: 0.1754 (tpt) cc_final: 0.1302 (tmt)
REVERT: A  219 ILE cc_start: 0.4485 (OUTLIER) cc_final: 0.3959 (pp)
REVERT: A  236 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.3241 (t80)
REVERT: A  245 GLN cc_start: 0.6723 (mp10) cc_final: 0.6055 (tt0)
  outliers start: 25
  outliers final: 15
  residues processed: 86
  average time/residue: 0.7947
  time to fit residues: 71.2504
Evaluate side-chains
  86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
C 138 GLN
C 148 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5609 r_free = 0.5609 target = 0.310086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5922 r_free = 0.5922 target = 0.272839 restraints weight = 31605.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.5499 rms_B_bonded: 5.13
r_work: 0.5869 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.5818 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.5818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5448 r_free = 0.5448    target_work(ls_wunit_k1) = 0.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5448 r_free = 0.5448    target_work(ls_wunit_k1) = 0.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5693
moved from start:          1.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3531  Z= 0.227
  Angle     :  1.038  11.229   4830  Z= 0.516
  Chirality :  0.061   0.279    606
  Planarity :  0.004   0.026    579
  Dihedral  : 13.249 100.411    711
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.53 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 33.33 %
    Favored  : 60.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.14 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS A 239 
 PHE   0.031   0.004   PHE C 237 
 TYR   0.019   0.003   TYR C 125 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00459 (   12)
  link_NAG-ASN         : angle       3.49097 (   36)
  hydrogen bonds       : bond        0.04922 (   53)
  hydrogen bonds       : angle       6.71234 (  156)
  SS BOND              : bond        0.00946 (    3)
  SS BOND              : angle       1.04002 (    6)
  covalent geometry    : bond        0.00517 ( 3516)
  covalent geometry    : angle       0.99667 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  184 ILE cc_start: 0.3831 (OUTLIER) cc_final: 0.3253 (pp)
REVERT: A  207 MET cc_start: 0.1777 (tpt) cc_final: 0.1336 (tmt)
REVERT: A  219 ILE cc_start: 0.4500 (OUTLIER) cc_final: 0.4014 (pp)
REVERT: A  236 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.3265 (t80)
REVERT: C  242 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6216 (mt0)
  outliers start: 23
  outliers final: 15
  residues processed: 83
  average time/residue: 0.7324
  time to fit residues: 63.5977
Evaluate side-chains
  83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  242 GLN
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    0.0010
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.7992

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5665 r_free = 0.5665 target = 0.319819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5978 r_free = 0.5978 target = 0.282731 restraints weight = 24621.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.5563 rms_B_bonded: 4.54
r_work: 0.5932 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.5882 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.5882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5513 r_free = 0.5513    target_work(ls_wunit_k1) = 0.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5513 r_free = 0.5513    target_work(ls_wunit_k1) = 0.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5545
moved from start:          1.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3531  Z= 0.164
  Angle     :  0.975  11.509   4830  Z= 0.477
  Chirality :  0.057   0.222    606
  Planarity :  0.003   0.024    579
  Dihedral  : 12.380  99.363    711
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 34.91 %
    Favored  : 60.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS A 239 
 PHE   0.030   0.003   PHE C 237 
 TYR   0.016   0.002   TYR A 125 
 ARG   0.001   0.000   ARG B 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00383 (   12)
  link_NAG-ASN         : angle       3.01209 (   36)
  hydrogen bonds       : bond        0.04349 (   53)
  hydrogen bonds       : angle       6.52664 (  156)
  SS BOND              : bond        0.00603 (    3)
  SS BOND              : angle       0.62323 (    6)
  covalent geometry    : bond        0.00365 ( 3516)
  covalent geometry    : angle       0.94334 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  157 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.4915 (t80)
REVERT: A  184 ILE cc_start: 0.4159 (OUTLIER) cc_final: 0.3690 (pp)
REVERT: A  207 MET cc_start: 0.1641 (tpt) cc_final: 0.1283 (tmt)
REVERT: A  219 ILE cc_start: 0.4285 (OUTLIER) cc_final: 0.3816 (pp)
REVERT: A  236 TYR cc_start: 0.6354 (p90) cc_final: 0.3425 (t80)
REVERT: A  245 GLN cc_start: 0.6727 (mp10) cc_final: 0.6212 (tt0)
REVERT: C  250 TYR cc_start: 0.5817 (OUTLIER) cc_final: 0.5281 (p90)
  outliers start: 16
  outliers final: 8
  residues processed: 81
  average time/residue: 0.8771
  time to fit residues: 73.8650
Evaluate side-chains
  78 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0050
   chunk 21 optimal weight:    0.0980
   chunk 32 optimal weight:   20.0000
   chunk 3 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN
C 156 ASN
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5667 r_free = 0.5667 target = 0.320230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5995 r_free = 0.5995 target = 0.284371 restraints weight = 30214.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.5562 rms_B_bonded: 5.04
r_work: 0.5919 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.5878 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.5878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5501 r_free = 0.5501    target_work(ls_wunit_k1) = 0.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5501 r_free = 0.5501    target_work(ls_wunit_k1) = 0.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.5501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5536
moved from start:          1.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3531  Z= 0.161
  Angle     :  0.952  11.239   4830  Z= 0.470
  Chirality :  0.057   0.215    606
  Planarity :  0.003   0.028    579
  Dihedral  : 12.041  97.372    711
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 34.91 %
    Favored  : 60.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.98 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS A 239 
 PHE   0.029   0.003   PHE C 237 
 TYR   0.017   0.002   TYR A 125 
 ARG   0.001   0.000   ARG C 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00375 (   12)
  link_NAG-ASN         : angle       2.94964 (   36)
  hydrogen bonds       : bond        0.04148 (   53)
  hydrogen bonds       : angle       6.54697 (  156)
  SS BOND              : bond        0.00637 (    3)
  SS BOND              : angle       0.69572 (    6)
  covalent geometry    : bond        0.00362 ( 3516)
  covalent geometry    : angle       0.92151 ( 4788)

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A  184 ILE cc_start: 0.4108 (OUTLIER) cc_final: 0.3658 (pp)
REVERT: A  219 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.3838 (pp)
REVERT: A  236 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.3470 (t80)
REVERT: A  245 GLN cc_start: 0.6550 (mp10) cc_final: 0.6220 (tt0)
REVERT: C  250 TYR cc_start: 0.5706 (OUTLIER) cc_final: 0.5160 (p90)
  outliers start: 18
  outliers final: 11
  residues processed: 81
  average time/residue: 0.7737
  time to fit residues: 65.2792
Evaluate side-chains
  85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  233 THR
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
C 138 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5619 r_free = 0.5619 target = 0.310514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5961 r_free = 0.5961 target = 0.273704 restraints weight = 32886.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.5509 rms_B_bonded: 5.19
r_work: 0.5873 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.5823 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.5823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5454 r_free = 0.5454    target_work(ls_wunit_k1) = 0.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5454 r_free = 0.5454    target_work(ls_wunit_k1) = 0.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.5454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5693
moved from start:          1.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3531  Z= 0.232
  Angle     :  1.067  10.780   4830  Z= 0.527
  Chirality :  0.061   0.273    606
  Planarity :  0.004   0.031    579
  Dihedral  : 12.251  96.297    711
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.78 %
    Favored  : 86.22 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 35.17 %
    Favored  : 59.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 239 
 PHE   0.027   0.004   PHE C 237 
 TYR   0.023   0.003   TYR C 125 
 ARG   0.002   0.001   ARG B 247 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00460 (   12)
  link_NAG-ASN         : angle       3.44307 (   36)
  hydrogen bonds       : bond        0.05104 (   53)
  hydrogen bonds       : angle       6.49753 (  156)
  SS BOND              : bond        0.01025 (    3)
  SS BOND              : angle       1.19208 (    6)
  covalent geometry    : bond        0.00535 ( 3516)
  covalent geometry    : angle       1.02881 ( 4788)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3348.66 seconds
wall clock time: 57 minutes 47.45 seconds (3467.45 seconds total)