Starting phenix.real_space_refine
on Wed Jul 23 15:25:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u12_26275/07_2025/7u12_26275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u12_26275/07_2025/7u12_26275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2025/7u12_26275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2025/7u12_26275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2025/7u12_26275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2025/7u12_26275.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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 1 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: 4.93, per 1000 atoms: 1.43
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (98.808, 118.14, 32.22, 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=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04

  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: 0.76
  Conformation dependent library (CDL) restraints added in 709.4 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, 64.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125
      removed outlier: 6.633A  pdb=" N   VAL A 123 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 9.036A  pdb=" N   SER A 130 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 9.415A  pdb=" N   VAL B 133 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   TYR A 132 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   TYR B 135 " --> pdb=" O   TYR A 132 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER A 134 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   VAL B 137 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ASP A 136 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   SER B 130 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
      removed outlier: 9.429A  pdb=" N   VAL C 133 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   TYR B 132 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   TYR C 135 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   SER B 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   VAL C 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASP B 136 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 165
      removed outlier: 5.950A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   ASN B 145 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   LEU A 144 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   THR B 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 8.959A  pdb=" N   ILE A 146 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 10.049A  pdb=" N   THR B 149 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 10.327A  pdb=" N   ASN B 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 9.030A  pdb=" N   LEU A 150 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 10.440A  pdb=" N   THR B 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 9.238A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 9.988A  pdb=" N   ASN B 155 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 8.994A  pdb=" N   ASN A 154 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 10.600A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   ASN A 156 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 9.896A  pdb=" N   SER B 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 9.371A  pdb=" N   TYR A 158 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 10.388A  pdb=" N   GLU B 161 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL A 160 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   GLU B 163 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL A 162 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   ILE B 165 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   ASN A 164 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   ILE B 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   ASN C 145 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   LEU B 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   THR C 147 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   ILE B 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 10.033A  pdb=" N   THR C 149 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 10.295A  pdb=" N   ASN C 151 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   LEU B 150 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 10.398A  pdb=" N   THR C 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 9.193A  pdb=" N   ILE B 152 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 9.935A  pdb=" N   ASN C 155 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   ASN B 154 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 10.542A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 8.981A  pdb=" N   ASN B 156 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   SER C 159 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 9.306A  pdb=" N   TYR B 158 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 10.323A  pdb=" N   GLU C 161 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   VAL B 160 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 8.808A  pdb=" N   GLU C 163 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL B 162 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE C 165 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ASN B 164 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.575A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.568A  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
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 8.946A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   TYR B 197 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ASP A 196 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 8.938A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 8.865A  pdb=" N   ILE C 195 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   GLN B 194 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   TYR C 197 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.405A  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: 6.452A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.502A  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: 6.952A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.025A  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: 6.991A  pdb=" N   HIS A 222 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 8.988A  pdb=" N   VAL B 225 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ILE A 224 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   MET B 227 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   HIS B 222 " --> pdb=" O   ASN C 223 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   VAL C 225 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE B 224 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   MET C 227 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU B 226 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.422A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   THR B 234 " --> pdb=" O   THR C 235 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   PHE C 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TYR B 236 " --> pdb=" O   PHE C 237 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   HIS C 239 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY B 238 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   GLU C 241 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER B 240 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ILE C 243 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   GLN C 245 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   SER B 244 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253
      removed outlier: 6.309A  pdb=" N   VAL A 251 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL B 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    36 hydrogen bonds defined for protein.
    108 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: 0.89

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1051
        1.34 -     1.46: 685
        1.46 -     1.57: 1741
        1.57 -     1.69: 3
        1.69 -     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  1.253  0.250 3.40e-02 8.65e+02 5.40e+01
  bond pdb=" CG  PRO A 189 "
       pdb=" CD  PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.253  0.250 3.40e-02 8.65e+02 5.39e+01
  bond pdb=" CG  PRO B 189 "
       pdb=" CD  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.255  0.248 3.40e-02 8.65e+02 5.34e+01
  bond pdb=" CB  PRO B 189 "
       pdb=" CG  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.669 -0.177 5.00e-02 4.00e+02 1.26e+01
  bond pdb=" CB  PRO C 189 "
       pdb=" CG  PRO C 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.669 -0.177 5.00e-02 4.00e+02 1.25e+01
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 4668
        2.78 -     5.55: 90
        5.55 -     8.33: 24
        8.33 -    11.10: 3
       11.10 -    13.88: 3
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" N   PRO C 189 "
        pdb=" CD  PRO C 189 "
        pdb=" CG  PRO C 189 "
      ideal   model   delta    sigma   weight residual
     103.20   89.32   13.88 1.50e+00 4.44e-01 8.56e+01
  angle pdb=" N   PRO A 189 "
        pdb=" CD  PRO A 189 "
        pdb=" CG  PRO A 189 "
      ideal   model   delta    sigma   weight residual
     103.20   89.34   13.86 1.50e+00 4.44e-01 8.53e+01
  angle pdb=" N   PRO B 189 "
        pdb=" CD  PRO B 189 "
        pdb=" CG  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     103.20   89.37   13.83 1.50e+00 4.44e-01 8.50e+01
  angle pdb=" N   PHE A 171 "
        pdb=" CA  PHE A 171 "
        pdb=" C   PHE A 171 "
      ideal   model   delta    sigma   weight residual
     108.96  115.81   -6.85 1.49e+00 4.50e-01 2.12e+01
  angle pdb=" N   PHE B 171 "
        pdb=" CA  PHE B 171 "
        pdb=" C   PHE B 171 "
      ideal   model   delta    sigma   weight residual
     108.96  115.78   -6.82 1.49e+00 4.50e-01 2.10e+01
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 1965
       16.69 -    33.37: 189
       33.37 -    50.06: 91
       50.06 -    66.74: 17
       66.74 -    83.43: 9
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  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   30.37   62.63     1      1.00e+01 1.00e-02 5.19e+01
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   30.37   62.63     1      1.00e+01 1.00e-02 5.19e+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   30.42   62.58     1      1.00e+01 1.00e-02 5.18e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 474
       0.081 -    0.162: 111
       0.162 -    0.243: 15
       0.243 -    0.324: 3
       0.324 -    0.405: 3
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CG  LEU A 226 "
            pdb=" CB  LEU A 226 "
            pdb=" CD1 LEU A 226 "
            pdb=" CD2 LEU A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.11e+00
  chirality pdb=" CG  LEU B 226 "
            pdb=" CB  LEU B 226 "
            pdb=" CD1 LEU B 226 "
            pdb=" CD2 LEU B 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.40 2.00e-01 2.50e+01 4.06e+00
  chirality pdb=" CG  LEU C 226 "
            pdb=" CB  LEU C 226 "
            pdb=" CD1 LEU C 226 "
            pdb=" CD2 LEU C 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.39 2.00e-01 2.50e+01 3.90e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 125 "   -0.004 2.00e-02 2.50e+03   2.41e-02 1.16e+01
        pdb=" CG  TYR A 125 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 125 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 125 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 125 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 125 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 125 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 125 "   -0.005 2.00e-02 2.50e+03   2.41e-02 1.16e+01
        pdb=" CG  TYR C 125 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 125 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 125 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 125 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 125 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 125 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 125 "   -0.004 2.00e-02 2.50e+03   2.39e-02 1.15e+01
        pdb=" CG  TYR B 125 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 125 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 125 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 125 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 125 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 125 "    0.007 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 86
        2.71 -     3.26: 3290
        3.26 -     3.80: 5387
        3.80 -     4.35: 6630
        4.35 -     4.90: 12470
  Nonbonded interactions: 27863
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 215 "
            pdb=" OD1 ASP B 212 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OG1 THR B 215 "
            pdb=" OD1 ASP C 212 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.279 3.120
  ... (remaining 27858 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 group one per residue
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:             2.190
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     16.180
  Find NCS groups from input model:        0.060
  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:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4439
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      :  0.011   0.250   3531  Z= 0.376
  Angle     :  1.183  13.880   4830  Z= 0.632
  Chirality :  0.072   0.405    606
  Planarity :  0.008   0.081    579
  Dihedral  : 16.716  83.426   1476
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  :  2.36 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B 239 
 PHE   0.045   0.007   PHE B 171 
 TYR   0.050   0.004   TYR C 125 
 ARG   0.008   0.002   ARG B 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00867 (   12)
  link_NAG-ASN         : angle       5.95531 (   36)
  hydrogen bonds       : bond        0.15526 (   36)
  hydrogen bonds       : angle       8.72436 (  108)
  SS BOND              : bond        0.00774 (    3)
  SS BOND              : angle       3.85040 (    6)
  covalent geometry    : bond        0.01092 ( 3516)
  covalent geometry    : angle       1.06082 ( 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
  130 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  178 LYS cc_start: 0.4567 (OUTLIER) cc_final: 0.3467 (mmpt)
REVERT: C  178 LYS cc_start: 0.4744 (OUTLIER) cc_final: 0.4489 (pptt)
REVERT: C  207 MET cc_start: 0.3545 (tmm) cc_final: 0.3187 (tmm)
  outliers start: 21
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1469
  time to fit residues: 20.2454
Evaluate side-chains
  73 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain C residue  178 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
A 245 GLN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5493 r_free = 0.5493 target = 0.322356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5627 r_free = 0.5627 target = 0.286687 restraints weight = 33287.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5592 r_free = 0.5592 target = 0.290458 restraints weight = 17289.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5600 r_free = 0.5600 target = 0.291770 restraints weight = 7082.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.5423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5423 r_free = 0.5423    target_work(ls_wunit_k1) = 0.313         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5421 r_free = 0.5421    target_work(ls_wunit_k1) = 0.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5347
moved from start:          0.5497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   3531  Z= 0.231
  Angle     :  1.012  12.952   4830  Z= 0.490
  Chirality :  0.061   0.420    606
  Planarity :  0.005   0.034    579
  Dihedral  :  8.277  52.908    719
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.12 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.34), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B 239 
 PHE   0.016   0.003   PHE A 213 
 TYR   0.024   0.003   TYR B 132 
 ARG   0.006   0.001   ARG B 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01148 (   12)
  link_NAG-ASN         : angle       6.10030 (   36)
  hydrogen bonds       : bond        0.04419 (   36)
  hydrogen bonds       : angle       6.90032 (  108)
  SS BOND              : bond        0.00920 (    3)
  SS BOND              : angle       2.91294 (    6)
  covalent geometry    : bond        0.00515 ( 3516)
  covalent geometry    : angle       0.86204 ( 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
  110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  216 LEU cc_start: 0.8256 (mp) cc_final: 0.7571 (tt)
REVERT: A  228 MET cc_start: 0.6825 (tmm) cc_final: 0.5719 (tpp)
REVERT: B  207 MET cc_start: 0.2965 (tmm) cc_final: 0.2488 (tmm)
REVERT: B  249 GLN cc_start: 0.6366 (tm-30) cc_final: 0.6135 (tm-30)
REVERT: C  172 SER cc_start: 0.7566 (t) cc_final: 0.7168 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1104
  time to fit residues: 14.5323
Evaluate side-chains
  92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   overall best weight:    2.1988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5501 r_free = 0.5501 target = 0.323354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.5731 r_free = 0.5731 target = 0.283854 restraints weight = 20650.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5689 r_free = 0.5689 target = 0.287180 restraints weight = 9071.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5691 r_free = 0.5691 target = 0.288695 restraints weight = 4417.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.5447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5447 r_free = 0.5447    target_work(ls_wunit_k1) = 0.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5447 r_free = 0.5447    target_work(ls_wunit_k1) = 0.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5413
moved from start:          0.6303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3531  Z= 0.153
  Angle     :  0.873  12.938   4830  Z= 0.410
  Chirality :  0.056   0.312    606
  Planarity :  0.003   0.027    579
  Dihedral  :  7.365  48.492    711
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 16.80 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.34), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B 239 
 PHE   0.021   0.003   PHE B 171 
 TYR   0.015   0.002   TYR B 250 
 ARG   0.003   0.001   ARG B 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01081 (   12)
  link_NAG-ASN         : angle       5.84465 (   36)
  hydrogen bonds       : bond        0.02958 (   36)
  hydrogen bonds       : angle       5.94292 (  108)
  SS BOND              : bond        0.00843 (    3)
  SS BOND              : angle       2.53742 (    6)
  covalent geometry    : bond        0.00344 ( 3516)
  covalent geometry    : angle       0.71022 ( 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
  94 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 MET cc_start: 0.6902 (tmm) cc_final: 0.5639 (tpp)
REVERT: B  207 MET cc_start: 0.3064 (tmm) cc_final: 0.2854 (tmm)
REVERT: C  172 SER cc_start: 0.7916 (t) cc_final: 0.7478 (m)
  outliers start: 13
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0982
  time to fit residues: 11.1516
Evaluate side-chains
  84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    0.0980
   chunk 7 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0970
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   overall best weight:    1.2382

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5512 r_free = 0.5512 target = 0.327867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5689 r_free = 0.5689 target = 0.288337 restraints weight = 26853.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5698 r_free = 0.5698 target = 0.293134 restraints weight = 14806.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5686 r_free = 0.5686 target = 0.293048 restraints weight = 6289.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.5449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5449 r_free = 0.5449    target_work(ls_wunit_k1) = 0.316         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5449 r_free = 0.5449    target_work(ls_wunit_k1) = 0.316         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5332
moved from start:          0.6790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3531  Z= 0.128
  Angle     :  0.816  12.380   4830  Z= 0.381
  Chirality :  0.055   0.288    606
  Planarity :  0.003   0.022    579
  Dihedral  :  6.041  32.090    711
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.06 %
    Favored  : 80.05 %
  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: -3.35 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 239 
 PHE   0.018   0.002   PHE B 171 
 TYR   0.008   0.001   TYR B 250 
 ARG   0.002   0.000   ARG B 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01065 (   12)
  link_NAG-ASN         : angle       5.50565 (   36)
  hydrogen bonds       : bond        0.03014 (   36)
  hydrogen bonds       : angle       5.62281 (  108)
  SS BOND              : bond        0.00525 (    3)
  SS BOND              : angle       1.86325 (    6)
  covalent geometry    : bond        0.00282 ( 3516)
  covalent geometry    : angle       0.66351 ( 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
  101 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: B  207 MET cc_start: 0.3058 (tmm) cc_final: 0.2825 (tmm)
REVERT: B  216 LEU cc_start: 0.6774 (tt) cc_final: 0.6513 (tt)
REVERT: C  157 TYR cc_start: 0.4161 (OUTLIER) cc_final: 0.2188 (p90)
REVERT: C  172 SER cc_start: 0.8002 (t) cc_final: 0.7631 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1036
  time to fit residues: 13.0982
Evaluate side-chains
  92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 TYR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    4.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 222 HIS
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5417 r_free = 0.5417 target = 0.309195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.5640 r_free = 0.5640 target = 0.268293 restraints weight = 23230.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.5665 r_free = 0.5665 target = 0.271048 restraints weight = 8668.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5679 r_free = 0.5679 target = 0.272771 restraints weight = 4792.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.5360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5359 r_free = 0.5359    target_work(ls_wunit_k1) = 0.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5359 r_free = 0.5359    target_work(ls_wunit_k1) = 0.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5659
moved from start:          0.8207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3531  Z= 0.217
  Angle     :  0.971  12.044   4830  Z= 0.466
  Chirality :  0.060   0.386    606
  Planarity :  0.003   0.018    579
  Dihedral  :  7.985  51.004    711
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.73 %
    Favored  : 76.38 %
  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: -3.60 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.016   0.003   PHE B 171 
 TYR   0.026   0.003   TYR C 158 
 ARG   0.004   0.001   ARG C 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01270 (   12)
  link_NAG-ASN         : angle       5.98135 (   36)
  hydrogen bonds       : bond        0.02997 (   36)
  hydrogen bonds       : angle       5.68950 (  108)
  SS BOND              : bond        0.00882 (    3)
  SS BOND              : angle       2.99431 (    6)
  covalent geometry    : bond        0.00494 ( 3516)
  covalent geometry    : angle       0.81919 ( 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
  99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  205 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5684 (pm20)
REVERT: B  207 MET cc_start: 0.3912 (tmm) cc_final: 0.3604 (tmm)
REVERT: C  172 SER cc_start: 0.8378 (t) cc_final: 0.8125 (m)
  outliers start: 11
  outliers final: 11
  residues processed: 93
  average time/residue: 0.1065
  time to fit residues: 13.0400
Evaluate side-chains
  92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 TYR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0980
   chunk 31 optimal weight:   30.0000
   chunk 17 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    1.1986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5490 r_free = 0.5490 target = 0.320501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.5655 r_free = 0.5655 target = 0.283094 restraints weight = 34197.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.5688 r_free = 0.5688 target = 0.286660 restraints weight = 17644.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5670 r_free = 0.5670 target = 0.287484 restraints weight = 7803.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.5417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5418 r_free = 0.5418    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 = 0.5418 r_free = 0.5418    target_work(ls_wunit_k1) = 0.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5438
moved from start:          0.8323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3531  Z= 0.133
  Angle     :  0.823  12.791   4830  Z= 0.389
  Chirality :  0.056   0.272    606
  Planarity :  0.002   0.016    579
  Dihedral  :  5.994  35.575    711
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.31 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 239 
 PHE   0.016   0.002   PHE B 171 
 TYR   0.015   0.001   TYR B 250 
 ARG   0.001   0.000   ARG B 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01112 (   12)
  link_NAG-ASN         : angle       5.52005 (   36)
  hydrogen bonds       : bond        0.02840 (   36)
  hydrogen bonds       : angle       5.13346 (  108)
  SS BOND              : bond        0.00559 (    3)
  SS BOND              : angle       2.93525 (    6)
  covalent geometry    : bond        0.00295 ( 3516)
  covalent geometry    : angle       0.66534 ( 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
  101 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.4676 (mm) cc_final: 0.4365 (pt)
REVERT: B  224 ILE cc_start: 0.6481 (mm) cc_final: 0.6190 (mm)
REVERT: C  157 TYR cc_start: 0.5633 (m-10) cc_final: 0.2927 (p90)
REVERT: C  172 SER cc_start: 0.8290 (t) cc_final: 0.8048 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1162
  time to fit residues: 14.3921
Evaluate side-chains
  89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.0770
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0870
   chunk 22 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.8322

-------------------------------------------------------------------------------
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 = 0.5450 r_free = 0.5450 target = 0.296210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5612 r_free = 0.5612 target = 0.271404 restraints weight = 25015.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5641 r_free = 0.5641 target = 0.274502 restraints weight = 8388.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.5661 r_free = 0.5661 target = 0.276404 restraints weight = 4449.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.5385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5384 r_free = 0.5384    target_work(ls_wunit_k1) = 0.286         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5384 r_free = 0.5384    target_work(ls_wunit_k1) = 0.286         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5532
moved from start:          0.8753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3531  Z= 0.142
  Angle     :  0.837  12.014   4830  Z= 0.396
  Chirality :  0.056   0.298    606
  Planarity :  0.003   0.021    579
  Dihedral  :  5.590  29.975    711
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.00 %
    Favored  : 76.12 %
  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: -3.40 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 239 
 PHE   0.016   0.002   PHE B 171 
 TYR   0.014   0.001   TYR C 158 
 ARG   0.001   0.000   ARG B 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01139 (   12)
  link_NAG-ASN         : angle       5.35427 (   36)
  hydrogen bonds       : bond        0.02846 (   36)
  hydrogen bonds       : angle       4.92665 (  108)
  SS BOND              : bond        0.00547 (    3)
  SS BOND              : angle       2.60150 (    6)
  covalent geometry    : bond        0.00319 ( 3516)
  covalent geometry    : angle       0.69445 ( 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
  100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A  121 ILE cc_start: 0.4766 (mm) cc_final: 0.4430 (pt)
REVERT: A  135 TYR cc_start: 0.5835 (m-10) cc_final: 0.4569 (p90)
REVERT: B  224 ILE cc_start: 0.6443 (mm) cc_final: 0.6130 (mm)
REVERT: C  157 TYR cc_start: 0.5744 (m-10) cc_final: 0.2919 (p90)
  outliers start: 11
  outliers final: 11
  residues processed: 94
  average time/residue: 0.1079
  time to fit residues: 13.4189
Evaluate side-chains
  94 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 22 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    2.6584

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

Flipped N/Q/H residues before XYZ refinement:
C 222 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5412 r_free = 0.5412 target = 0.291789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5581 r_free = 0.5581 target = 0.265863 restraints weight = 30716.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5618 r_free = 0.5618 target = 0.269366 restraints weight = 8566.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5640 r_free = 0.5640 target = 0.271485 restraints weight = 4263.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.5352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5352 r_free = 0.5352    target_work(ls_wunit_k1) = 0.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5352 r_free = 0.5352    target_work(ls_wunit_k1) = 0.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5607
moved from start:          0.9331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3531  Z= 0.162
  Angle     :  0.885  12.197   4830  Z= 0.419
  Chirality :  0.056   0.305    606
  Planarity :  0.002   0.015    579
  Dihedral  :  5.979  32.767    711
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 22.57 %
    Favored  : 73.75 %
  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: -3.55 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 239 
 PHE   0.015   0.002   PHE B 171 
 TYR   0.016   0.002   TYR C 158 
 ARG   0.002   0.001   ARG B 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01197 (   12)
  link_NAG-ASN         : angle       5.48419 (   36)
  hydrogen bonds       : bond        0.02961 (   36)
  hydrogen bonds       : angle       4.71883 (  108)
  SS BOND              : bond        0.00717 (    3)
  SS BOND              : angle       2.84493 (    6)
  covalent geometry    : bond        0.00370 ( 3516)
  covalent geometry    : angle       0.74363 ( 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
  98 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  121 ILE cc_start: 0.5095 (mm) cc_final: 0.4818 (pt)
REVERT: A  135 TYR cc_start: 0.5901 (m-10) cc_final: 0.4621 (p90)
REVERT: A  205 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5584 (pm20)
REVERT: B  224 ILE cc_start: 0.6305 (mm) cc_final: 0.5984 (mm)
  outliers start: 14
  outliers final: 14
  residues processed: 91
  average time/residue: 0.0921
  time to fit residues: 11.3972
Evaluate side-chains
  97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  171 PHE
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 14 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.5349 r_free = 0.5349 target = 0.278661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5571 r_free = 0.5571 target = 0.253782 restraints weight = 20250.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.5551 r_free = 0.5551 target = 0.257077 restraints weight = 7148.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5554 r_free = 0.5554 target = 0.258072 restraints weight = 4026.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.5290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5290 r_free = 0.5290    target_work(ls_wunit_k1) = 0.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5290 r_free = 0.5290    target_work(ls_wunit_k1) = 0.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5817
moved from start:          1.0296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3531  Z= 0.264
  Angle     :  1.062  13.920   4830  Z= 0.513
  Chirality :  0.062   0.401    606
  Planarity :  0.004   0.027    579
  Dihedral  :  8.925  59.721    711
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 21.78 %
    Favored  : 73.23 %
  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: -3.91 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.024   0.003   PHE A 237 
 TYR   0.027   0.004   TYR C 158 
 ARG   0.004   0.001   ARG A 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01483 (   12)
  link_NAG-ASN         : angle       6.22527 (   36)
  hydrogen bonds       : bond        0.03872 (   36)
  hydrogen bonds       : angle       5.15795 (  108)
  SS BOND              : bond        0.01301 (    3)
  SS BOND              : angle       3.94759 (    6)
  covalent geometry    : bond        0.00595 ( 3516)
  covalent geometry    : angle       0.90950 ( 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
  105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  135 TYR cc_start: 0.6050 (m-10) cc_final: 0.4940 (p90)
REVERT: A  157 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5404 (m-10)
REVERT: A  205 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5841 (pm20)
REVERT: B  171 PHE cc_start: 0.6344 (p90) cc_final: 0.6032 (t80)
REVERT: B  224 ILE cc_start: 0.6620 (mm) cc_final: 0.6286 (mm)
  outliers start: 19
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0961
  time to fit residues: 12.1856
Evaluate side-chains
  93 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
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:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.5359 r_free = 0.5359 target = 0.280066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5553 r_free = 0.5553 target = 0.254101 restraints weight = 24285.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.5586 r_free = 0.5586 target = 0.257192 restraints weight = 7541.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5605 r_free = 0.5605 target = 0.259056 restraints weight = 3899.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.5297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5297 r_free = 0.5297    target_work(ls_wunit_k1) = 0.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5297 r_free = 0.5297    target_work(ls_wunit_k1) = 0.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5297
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5802
moved from start:          1.0451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3531  Z= 0.229
  Angle     :  1.013  13.465   4830  Z= 0.487
  Chirality :  0.060   0.363    606
  Planarity :  0.003   0.022    579
  Dihedral  :  8.288  50.443    711
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.15 %
    Favored  : 72.70 %
  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: -3.97 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.023   0.003   PHE A 237 
 TYR   0.021   0.003   TYR C 158 
 ARG   0.003   0.001   ARG A 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01424 (   12)
  link_NAG-ASN         : angle       6.02212 (   36)
  hydrogen bonds       : bond        0.03738 (   36)
  hydrogen bonds       : angle       5.06681 (  108)
  SS BOND              : bond        0.01080 (    3)
  SS BOND              : angle       3.51218 (    6)
  covalent geometry    : bond        0.00520 ( 3516)
  covalent geometry    : angle       0.86472 ( 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: 12
    poor density    : 78
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  135 TYR cc_start: 0.5885 (m-10) cc_final: 0.4780 (p90)
REVERT: A  205 GLU cc_start: 0.6580 (mm-30) cc_final: 0.5797 (pm20)
REVERT: B  171 PHE cc_start: 0.6264 (p90) cc_final: 0.6037 (t80)
REVERT: B  224 ILE cc_start: 0.6559 (mm) cc_final: 0.6208 (mm)
  outliers start: 12
  outliers final: 12
  residues processed: 86
  average time/residue: 0.1016
  time to fit residues: 11.9312
Evaluate side-chains
  90 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  213 PHE
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.5410 r_free = 0.5410 target = 0.289183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5588 r_free = 0.5588 target = 0.263422 restraints weight = 31523.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5626 r_free = 0.5626 target = 0.266917 restraints weight = 8675.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5647 r_free = 0.5647 target = 0.269024 restraints weight = 4187.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.5348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5348 r_free = 0.5348    target_work(ls_wunit_k1) = 0.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5348 r_free = 0.5348    target_work(ls_wunit_k1) = 0.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5641
moved from start:          1.0361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3531  Z= 0.146
  Angle     :  0.898  12.733   4830  Z= 0.420
  Chirality :  0.056   0.290    606
  Planarity :  0.002   0.016    579
  Dihedral  :  6.681  38.023    711
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 25.72 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 239 
 PHE   0.015   0.002   PHE B 171 
 TYR   0.013   0.001   TYR C 158 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01234 (   12)
  link_NAG-ASN         : angle       5.62571 (   36)
  hydrogen bonds       : bond        0.03222 (   36)
  hydrogen bonds       : angle       4.63913 (  108)
  SS BOND              : bond        0.00660 (    3)
  SS BOND              : angle       2.45485 (    6)
  covalent geometry    : bond        0.00326 ( 3516)
  covalent geometry    : angle       0.75380 ( 4788)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1691.84 seconds
wall clock time: 30 minutes 4.06 seconds (1804.06 seconds total)