Starting phenix.real_space_refine
on Fri Aug 22 15:01:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnb_50587/08_2025/9fnb_50587_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnb_50587/08_2025/9fnb_50587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnb_50587/08_2025/9fnb_50587_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnb_50587/08_2025/9fnb_50587_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fnb_50587/08_2025/9fnb_50587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnb_50587/08_2025/9fnb_50587.map"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      28      5.16       5
     C    2904      2.51       5
     N     708      2.21       5
     O     928      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4568
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    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
  Restraints were copied for chains:
    A, C, D
  Time building chain proxies: 0.91, per 1000 atoms: 0.20
  Number of scatterers: 4568
  At special positions: 0
  Unit cell: (102.176, 104.648, 37.08, 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      28     16.00
     O     928      8.00
     N     708      7.00
     C    2904      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS D 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 145 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 145 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 145 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 164 "
      " NAG D 301 " - " ASN D 145 "
      " NAG D 302 " - " ASN D 151 "
      " NAG D 303 " - " ASN D 164 "
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 124.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 74.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126
      removed outlier: 6.961A  pdb=" N   ASP A 122 " --> pdb=" O   ILE C 121 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ILE B 121 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
      removed outlier: 8.872A  pdb=" N   LYS C 124 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL B 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   ILE C 126 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   TYR B 125 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ASP B 122 " --> pdb=" O   ILE D 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130
      removed outlier: 6.659A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.817A  pdb=" N   VAL A 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL B 133 " --> pdb=" O   SER D 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 176
      removed outlier: 7.046A  pdb=" N   ILE A 142 " --> pdb=" O   THR C 141 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   TYR C 143 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   LEU A 144 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ASN C 145 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL A 162 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLU C 163 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ASN A 164 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE C 165 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   THR A 166 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
      removed outlier: 9.327A  pdb=" N   THR B 141 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 9.584A  pdb=" N   LEU C 144 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 8.992A  pdb=" N   TYR B 143 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 9.232A  pdb=" N   ILE C 146 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASN B 145 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   ASN C 148 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR B 147 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   LEU C 150 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   THR B 149 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ILE C 152 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ASN B 151 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ASN C 154 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   THR B 153 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   ASN C 156 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ASN B 155 " --> pdb=" O   ASN C 156 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   TYR C 158 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TYR B 157 " --> pdb=" O   TYR C 158 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   VAL C 160 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER B 159 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   VAL C 162 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   GLU B 161 " --> pdb=" O   VAL C 162 " (cutoff:3.500A)
      removed outlier: 9.933A  pdb=" N   ASN C 164 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 9.567A  pdb=" N   GLU B 163 " --> pdb=" O   ASN C 164 " (cutoff:3.500A)
      removed outlier: 9.980A  pdb=" N   THR C 166 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ILE B 165 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   GLN C 168 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA B 167 " --> pdb=" O   GLN C 168 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   GLN C 170 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   VAL B 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   SER C 172 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   PHE B 171 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   THR C 174 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   LYS B 173 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   ILE C 176 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL B 175 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE B 142 " --> pdb=" O   THR D 141 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   TYR D 143 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   LEU B 144 " --> pdb=" O   TYR D 143 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ASN D 145 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL B 162 " --> pdb=" O   GLU D 161 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLU D 163 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ASN B 164 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE D 165 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   THR B 166 " --> pdb=" O   ILE D 165 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 187
      removed outlier: 6.953A  pdb=" N   ILE C 184 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   THR A 185 " --> pdb=" O   ILE C 184 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ILE C 186 " --> pdb=" O   THR A 185 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE A 187 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   ASN C 183 " --> pdb=" O   ARG B 180 " (cutoff:3.500A)
      removed outlier: 8.766A  pdb=" N   ASN B 182 " --> pdb=" O   ASN C 183 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   THR C 185 " --> pdb=" O   ASN B 182 " (cutoff:3.500A)
      removed outlier: 9.106A  pdb=" N   ILE B 184 " --> pdb=" O   THR C 185 " (cutoff:3.500A)
      removed outlier: 10.253A  pdb=" N   ILE C 187 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 9.027A  pdb=" N   ILE B 186 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ILE D 184 " --> pdb=" O   ASN B 183 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   THR B 185 " --> pdb=" O   ILE D 184 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ILE D 186 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ILE B 187 " --> pdb=" O   ILE D 186 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 191 through 198
      removed outlier: 6.898A  pdb=" N   ILE C 195 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ASP A 196 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   TYR C 197 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   THR A 198 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ASP B 191 " --> pdb=" O   MET C 192 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   GLN C 194 " --> pdb=" O   ASP B 191 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   LYS B 193 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ASP C 196 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 9.142A  pdb=" N   ILE B 195 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 10.374A  pdb=" N   THR C 198 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 9.318A  pdb=" N   TYR B 197 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ILE D 195 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ASP B 196 " --> pdb=" O   ILE D 195 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   TYR D 197 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   THR B 198 " --> pdb=" O   TYR D 197 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 206
      removed outlier: 6.458A  pdb=" N   THR A 201 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   ALA C 204 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A 203 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   GLU C 206 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLU A 205 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   THR B 201 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   ALA D 204 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ILE B 203 " --> pdb=" O   ALA D 204 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   GLU D 206 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU B 205 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 209 through 230
      removed outlier: 9.190A  pdb=" N   TYR A 209 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
      removed outlier: 10.599A  pdb=" N   ASP C 212 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 9.160A  pdb=" N   TYR A 211 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 10.176A  pdb=" N   CYS C 214 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   PHE A 213 " --> pdb=" O   CYS C 214 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   LEU C 216 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   THR A 215 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   SER C 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE A 217 " --> pdb=" O   SER C 218 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   LYS C 220 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   ILE A 219 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   HIS C 222 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 9.218A  pdb=" N   VAL A 221 " --> pdb=" O   HIS C 222 " (cutoff:3.500A)
      removed outlier: 9.738A  pdb=" N   ILE C 224 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ASN A 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LEU C 226 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL A 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   MET C 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   MET A 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   VAL C 230 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   GLN A 229 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   PHE C 213 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   CYS B 214 " --> pdb=" O   PHE C 213 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL C 221 " --> pdb=" O   LYS B 220 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   HIS B 222 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ASN C 223 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   VAL B 230 " --> pdb=" O   GLN C 229 " (cutoff:3.500A)
      removed outlier: 9.190A  pdb=" N   TYR B 209 " --> pdb=" O   MET D 210 " (cutoff:3.500A)
      removed outlier: 10.600A  pdb=" N   ASP D 212 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 9.160A  pdb=" N   TYR B 211 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
      removed outlier: 10.176A  pdb=" N   CYS D 214 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   PHE B 213 " --> pdb=" O   CYS D 214 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   LEU D 216 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   THR B 215 " --> pdb=" O   LEU D 216 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   SER D 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE B 217 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   LYS D 220 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   ILE B 219 " --> pdb=" O   LYS D 220 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   HIS D 222 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 9.217A  pdb=" N   VAL B 221 " --> pdb=" O   HIS D 222 " (cutoff:3.500A)
      removed outlier: 9.738A  pdb=" N   ILE D 224 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ASN B 223 " --> pdb=" O   ILE D 224 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LEU D 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL B 225 " --> pdb=" O   LEU D 226 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   MET D 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   MET B 227 " --> pdb=" O   MET D 228 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   VAL D 230 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   GLN B 229 " --> pdb=" O   VAL D 230 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 233 through 252
      removed outlier: 6.548A  pdb=" N   THR A 233 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   TYR C 236 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   THR A 235 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   GLY C 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   PHE A 237 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   SER C 240 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   HIS A 239 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   GLN C 242 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLU A 241 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   SER C 244 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE A 243 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   GLU C 246 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLN A 245 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   TYR C 248 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ARG A 247 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   TYR C 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 8.966A  pdb=" N   GLN A 249 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ASP C 252 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 9.430A  pdb=" N   VAL A 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL C 251 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ASP B 252 " --> pdb=" O   VAL C 251 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   THR B 233 " --> pdb=" O   THR D 234 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   TYR D 236 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   THR B 235 " --> pdb=" O   TYR D 236 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   GLY D 238 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   PHE B 237 " --> pdb=" O   GLY D 238 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   SER D 240 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   HIS B 239 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   GLN D 242 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLU B 241 " --> pdb=" O   GLN D 242 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   SER D 244 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE B 243 " --> pdb=" O   SER D 244 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   GLU D 246 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLN B 245 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   TYR D 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ARG B 247 " --> pdb=" O   TYR D 248 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   TYR D 250 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 8.966A  pdb=" N   GLN B 249 " --> pdb=" O   TYR D 250 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ASP D 252 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 9.430A  pdb=" N   VAL B 251 " --> pdb=" O   ASP D 252 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    327 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: 0.47

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1137
        1.34 -     1.46: 1377
        1.46 -     1.58: 2078
        1.58 -     1.70: 0
        1.70 -     1.83: 48
  Bond restraints: 4640
  Sorted by residual:
  bond pdb=" CG  HIS C 222 "
       pdb=" CD2 HIS C 222 "
    ideal  model  delta    sigma   weight residual
    1.354  1.329  0.025 1.10e-02 8.26e+03 5.13e+00
  bond pdb=" CA  ALA C 167 "
       pdb=" CB  ALA C 167 "
    ideal  model  delta    sigma   weight residual
    1.532  1.491  0.040 1.82e-02 3.02e+03 4.95e+00
  bond pdb=" CG  HIS D 222 "
       pdb=" CD2 HIS D 222 "
    ideal  model  delta    sigma   weight residual
    1.354  1.330  0.024 1.10e-02 8.26e+03 4.84e+00
  bond pdb=" CG  HIS B 222 "
       pdb=" CD2 HIS B 222 "
    ideal  model  delta    sigma   weight residual
    1.354  1.330  0.024 1.10e-02 8.26e+03 4.81e+00
  bond pdb=" CA  ALA D 167 "
       pdb=" CB  ALA D 167 "
    ideal  model  delta    sigma   weight residual
    1.532  1.492  0.040 1.82e-02 3.02e+03 4.78e+00
  ... (remaining 4635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 4936
        1.43 -     2.86: 1122
        2.86 -     4.29: 176
        4.29 -     5.71: 54
        5.71 -     7.14: 20
  Bond angle restraints: 6308
  Sorted by residual:
  angle pdb=" N   ASN A 151 "
        pdb=" CA  ASN A 151 "
        pdb=" CB  ASN A 151 "
      ideal   model   delta    sigma   weight residual
     110.87  103.73    7.14 1.63e+00 3.76e-01 1.92e+01
  angle pdb=" N   ASN B 151 "
        pdb=" CA  ASN B 151 "
        pdb=" CB  ASN B 151 "
      ideal   model   delta    sigma   weight residual
     110.87  103.74    7.13 1.63e+00 3.76e-01 1.91e+01
  angle pdb=" N   ASN C 151 "
        pdb=" CA  ASN C 151 "
        pdb=" CB  ASN C 151 "
      ideal   model   delta    sigma   weight residual
     110.87  103.75    7.12 1.63e+00 3.76e-01 1.91e+01
  angle pdb=" N   ASN D 151 "
        pdb=" CA  ASN D 151 "
        pdb=" CB  ASN D 151 "
      ideal   model   delta    sigma   weight residual
     110.87  103.76    7.11 1.63e+00 3.76e-01 1.90e+01
  angle pdb=" N   GLU B 246 "
        pdb=" CA  GLU B 246 "
        pdb=" C   GLU B 246 "
      ideal   model   delta    sigma   weight residual
     108.79  114.65   -5.86 1.53e+00 4.27e-01 1.47e+01
  ... (remaining 6303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.98: 2519
       12.98 -    25.97: 341
       25.97 -    38.95: 72
       38.95 -    51.93: 20
       51.93 -    64.91: 44
  Dihedral angle restraints: 2996
    sinusoidal: 1372
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" CA  THR C 234 "
           pdb=" C   THR C 234 "
           pdb=" N   THR C 235 "
           pdb=" CA  THR C 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.39   21.61     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  THR B 234 "
           pdb=" C   THR B 234 "
           pdb=" N   THR B 235 "
           pdb=" CA  THR B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.40   21.60     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  THR D 234 "
           pdb=" C   THR D 234 "
           pdb=" N   THR D 235 "
           pdb=" CA  THR D 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.42   21.58     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2993 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.253: 788
       0.253 -    0.507: 0
       0.507 -    0.760: 0
       0.760 -    1.014: 4
       1.014 -    1.267: 8
  Chirality restraints: 800
  Sorted by residual:
  chirality pdb=" C1  NAG D 303 "
            pdb=" ND2 ASN D 164 "
            pdb=" C2  NAG D 303 "
            pdb=" O5  NAG D 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.13   -1.27 2.00e-01 2.50e+01 4.01e+01
  chirality pdb=" C1  NAG C 303 "
            pdb=" ND2 ASN C 164 "
            pdb=" C2  NAG C 303 "
            pdb=" O5  NAG C 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.13   -1.27 2.00e-01 2.50e+01 4.01e+01
  chirality pdb=" C1  NAG B 303 "
            pdb=" ND2 ASN B 164 "
            pdb=" C2  NAG B 303 "
            pdb=" O5  NAG B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.13   -1.27 2.00e-01 2.50e+01 4.01e+01
  ... (remaining 797 not shown)

  Planarity restraints: 772
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 301 "    0.052 2.00e-02 2.50e+03   4.32e-02 2.33e+01
        pdb=" C7  NAG D 301 "   -0.009 2.00e-02 2.50e+03
        pdb=" C8  NAG D 301 "    0.038 2.00e-02 2.50e+03
        pdb=" N2  NAG D 301 "   -0.070 2.00e-02 2.50e+03
        pdb=" O7  NAG D 301 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 301 "    0.052 2.00e-02 2.50e+03   4.30e-02 2.31e+01
        pdb=" C7  NAG C 301 "   -0.009 2.00e-02 2.50e+03
        pdb=" C8  NAG C 301 "    0.038 2.00e-02 2.50e+03
        pdb=" N2  NAG C 301 "   -0.070 2.00e-02 2.50e+03
        pdb=" O7  NAG C 301 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 301 "    0.052 2.00e-02 2.50e+03   4.29e-02 2.30e+01
        pdb=" C7  NAG B 301 "   -0.009 2.00e-02 2.50e+03
        pdb=" C8  NAG B 301 "    0.038 2.00e-02 2.50e+03
        pdb=" N2  NAG B 301 "   -0.070 2.00e-02 2.50e+03
        pdb=" O7  NAG B 301 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 769 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1061
        2.83 -     3.35: 3659
        3.35 -     3.86: 7908
        3.86 -     4.38: 8522
        4.38 -     4.90: 16518
  Nonbonded interactions: 37668
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 231 "
            pdb=" OG1 THR D 234 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR A 231 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR B 231 "
            pdb=" OG1 THR B 234 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR C 231 "
            pdb=" OG1 THR C 234 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD1 ASN D 182 "
            pdb=" ND2 ASN D 183 "
     model   vdw
     2.440 3.120
  ... (remaining 37663 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:8.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
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      :  0.009   0.094   4656  Z= 0.544
  Angle     :  1.410  12.087   6352  Z= 0.821
  Chirality :  0.161   1.267    800
  Planarity :  0.009   0.043    760
  Dihedral  : 15.189  64.911   1944
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.94 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.002   ARG A 247 
 TYR   0.028   0.007   TYR D 248 
 PHE   0.019   0.006   PHE B 237 
 HIS   0.006   0.003   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00828 ( 4640)
  covalent geometry    : angle       1.33889 ( 6308)
  SS BOND              : bond        0.01129 (    4)
  SS BOND              : angle       2.84140 (    8)
  hydrogen bonds       : bond        0.16750 (  109)
  hydrogen bonds       : angle       8.12044 (  327)
  link_NAG-ASN         : bond        0.07426 (   12)
  link_NAG-ASN         : angle       5.91166 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8370 (mm-40)
REVERT: B  192 MET cc_start: 0.8646 (mtp) cc_final: 0.8418 (mtm)
REVERT: D  180 ARG cc_start: 0.8461 (mmt-90) cc_final: 0.8252 (mpt180)
REVERT: D  192 MET cc_start: 0.8895 (mtp) cc_final: 0.8675 (mtm)
REVERT: D  206 GLU cc_start: 0.8820 (tt0) cc_final: 0.8610 (tt0)
REVERT: D  207 MET cc_start: 0.9091 (mtp) cc_final: 0.8870 (mtp)
REVERT: D  228 MET cc_start: 0.9275 (ttm) cc_final: 0.9043 (ttm)
  outliers start: 4
  outliers final: 0
  residues processed: 118
  average time/residue: 0.6631
  time to fit residues: 80.3046
Evaluate side-chains
  108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   overall best weight:    2.3904

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
A 138 GLN
A 229 GLN
C 229 GLN
D 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.109604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.088598 restraints weight = 5310.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.00
r_work: 0.3229 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4656  Z= 0.157
  Angle     :  0.601   4.893   6352  Z= 0.327
  Chirality :  0.051   0.141    800
  Planarity :  0.003   0.017    760
  Dihedral  :  6.900  44.028    932
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.10 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.27 (0.33), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.017   0.002   TYR A 143 
 PHE   0.011   0.002   PHE C 237 
 HIS   0.006   0.003   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 4640)
  covalent geometry    : angle       0.59141 ( 6308)
  SS BOND              : bond        0.00107 (    4)
  SS BOND              : angle       0.54238 (    8)
  hydrogen bonds       : bond        0.03060 (  109)
  hydrogen bonds       : angle       6.14421 (  327)
  link_NAG-ASN         : bond        0.00077 (   12)
  link_NAG-ASN         : angle       1.55558 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  192 MET cc_start: 0.8392 (mtp) cc_final: 0.8082 (mtm)
REVERT: B  207 MET cc_start: 0.8786 (mtp) cc_final: 0.8561 (mtm)
REVERT: C  206 GLU cc_start: 0.8385 (tt0) cc_final: 0.8180 (tt0)
REVERT: D  124 LYS cc_start: 0.9254 (mttt) cc_final: 0.8986 (mttm)
REVERT: D  139 LYS cc_start: 0.8139 (ttmt) cc_final: 0.6997 (mmpt)
REVERT: D  192 MET cc_start: 0.8689 (mtp) cc_final: 0.8405 (mtm)
REVERT: D  207 MET cc_start: 0.8981 (mtp) cc_final: 0.8632 (mtp)
  outliers start: 7
  outliers final: 0
  residues processed: 111
  average time/residue: 0.6520
  time to fit residues: 74.3137
Evaluate side-chains
  108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
B 194 GLN
A 138 GLN
A 229 GLN
C 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.107260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.086432 restraints weight = 5355.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.00
r_work: 0.3202 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4656  Z= 0.220
  Angle     :  0.648   5.119   6352  Z= 0.349
  Chirality :  0.052   0.132    800
  Planarity :  0.003   0.027    760
  Dihedral  :  6.720  30.115    932
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.90 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.33), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.017   0.002   TYR C 143 
 PHE   0.013   0.003   PHE D 171 
 HIS   0.005   0.003   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 4640)
  covalent geometry    : angle       0.63710 ( 6308)
  SS BOND              : bond        0.00090 (    4)
  SS BOND              : angle       0.66163 (    8)
  hydrogen bonds       : bond        0.03156 (  109)
  hydrogen bonds       : angle       5.92707 (  327)
  link_NAG-ASN         : bond        0.00126 (   12)
  link_NAG-ASN         : angle       1.70134 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8171 (mtpt)
REVERT: B  192 MET cc_start: 0.8406 (mtp) cc_final: 0.8078 (mtm)
REVERT: B  207 MET cc_start: 0.8763 (mtp) cc_final: 0.8525 (mtm)
REVERT: C  206 GLU cc_start: 0.8444 (tt0) cc_final: 0.8223 (tt0)
REVERT: D  139 LYS cc_start: 0.8252 (ttmt) cc_final: 0.6910 (tppt)
REVERT: D  192 MET cc_start: 0.8677 (mtp) cc_final: 0.8382 (mtm)
REVERT: D  207 MET cc_start: 0.9044 (mtp) cc_final: 0.8692 (mtp)
REVERT: D  209 TYR cc_start: 0.7938 (m-80) cc_final: 0.7693 (m-80)
  outliers start: 9
  outliers final: 0
  residues processed: 117
  average time/residue: 0.6834
  time to fit residues: 82.0384
Evaluate side-chains
  113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0170
   overall best weight:    2.0022

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 229 GLN
C 138 GLN
C 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.110323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.089302 restraints weight = 5236.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.01
r_work: 0.3251 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4656  Z= 0.134
  Angle     :  0.569   6.247   6352  Z= 0.306
  Chirality :  0.050   0.131    800
  Planarity :  0.002   0.014    760
  Dihedral  :  6.042  24.220    932
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.10 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.014   0.002   TYR A 143 
 PHE   0.013   0.002   PHE C 213 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4640)
  covalent geometry    : angle       0.55749 ( 6308)
  SS BOND              : bond        0.00081 (    4)
  SS BOND              : angle       0.38034 (    8)
  hydrogen bonds       : bond        0.02482 (  109)
  hydrogen bonds       : angle       5.57171 (  327)
  link_NAG-ASN         : bond        0.00063 (   12)
  link_NAG-ASN         : angle       1.62413 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8038 (ptpt)
REVERT: B  178 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8088 (mtpt)
REVERT: B  192 MET cc_start: 0.8389 (mtp) cc_final: 0.8079 (mtm)
REVERT: D  139 LYS cc_start: 0.8209 (ttmt) cc_final: 0.6975 (tppt)
REVERT: D  192 MET cc_start: 0.8663 (mtp) cc_final: 0.8334 (mtm)
REVERT: D  209 TYR cc_start: 0.7912 (m-80) cc_final: 0.7710 (m-80)
  outliers start: 8
  outliers final: 0
  residues processed: 116
  average time/residue: 0.7040
  time to fit residues: 83.7200
Evaluate side-chains
  111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   overall best weight:    5.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
A 138 GLN
A 229 GLN
C 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.105420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.084779 restraints weight = 5408.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.99
r_work: 0.3179 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.039   4656  Z= 0.325
  Angle     :  0.723   7.332   6352  Z= 0.385
  Chirality :  0.053   0.134    800
  Planarity :  0.004   0.039    760
  Dihedral  :  7.435  39.940    932
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.09 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.32 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 247 
 TYR   0.019   0.003   TYR C 135 
 PHE   0.015   0.003   PHE B 171 
 HIS   0.005   0.003   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 ( 4640)
  covalent geometry    : angle       0.71125 ( 6308)
  SS BOND              : bond        0.00186 (    4)
  SS BOND              : angle       0.75154 (    8)
  hydrogen bonds       : bond        0.03549 (  109)
  hydrogen bonds       : angle       5.89113 (  327)
  link_NAG-ASN         : bond        0.00215 (   12)
  link_NAG-ASN         : angle       1.88647 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8201 (mtpt)
REVERT: B  192 MET cc_start: 0.8384 (mtp) cc_final: 0.8063 (mtm)
REVERT: A  228 MET cc_start: 0.9424 (ttm) cc_final: 0.9213 (ttm)
REVERT: D  139 LYS cc_start: 0.8366 (ttmt) cc_final: 0.6877 (tppt)
REVERT: D  192 MET cc_start: 0.8673 (mtp) cc_final: 0.8359 (mtm)
REVERT: D  209 TYR cc_start: 0.7989 (m-80) cc_final: 0.7586 (m-80)
  outliers start: 9
  outliers final: 1
  residues processed: 121
  average time/residue: 0.7002
  time to fit residues: 86.9539
Evaluate side-chains
  119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  224 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 8 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
B 182 ASN
B 183 ASN
B 194 GLN
A 138 GLN
A 182 ASN
A 183 ASN
A 229 GLN
C 138 GLN
C 182 ASN
C 183 ASN
C 229 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.110388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.089339 restraints weight = 5405.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.03
r_work: 0.3259 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4656  Z= 0.123
  Angle     :  0.574   8.270   6352  Z= 0.305
  Chirality :  0.050   0.128    800
  Planarity :  0.002   0.018    760
  Dihedral  :  6.114  26.560    932
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 16.67 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.014   0.002   TYR A 143 
 PHE   0.017   0.002   PHE C 213 
 HIS   0.005   0.002   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4640)
  covalent geometry    : angle       0.56112 ( 6308)
  SS BOND              : bond        0.00073 (    4)
  SS BOND              : angle       0.39244 (    8)
  hydrogen bonds       : bond        0.02303 (  109)
  hydrogen bonds       : angle       5.46854 (  327)
  link_NAG-ASN         : bond        0.00071 (   12)
  link_NAG-ASN         : angle       1.70848 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  144 LEU cc_start: 0.8780 (tt) cc_final: 0.8554 (tt)
REVERT: B  178 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8118 (mtpt)
REVERT: B  192 MET cc_start: 0.8385 (mtp) cc_final: 0.8046 (mtm)
REVERT: C  192 MET cc_start: 0.8484 (mtp) cc_final: 0.8262 (mtm)
REVERT: D  139 LYS cc_start: 0.8226 (ttmt) cc_final: 0.6884 (tppt)
REVERT: D  192 MET cc_start: 0.8654 (mtp) cc_final: 0.8321 (mtm)
REVERT: D  207 MET cc_start: 0.9086 (mtp) cc_final: 0.8701 (mtp)
REVERT: D  209 TYR cc_start: 0.7916 (m-80) cc_final: 0.7616 (m-80)
  outliers start: 4
  outliers final: 0
  residues processed: 114
  average time/residue: 0.6378
  time to fit residues: 74.6589
Evaluate side-chains
  108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0970
   chunk 38 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    2.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
B 194 GLN
A 138 GLN
A 229 GLN
C 138 GLN
C 229 GLN
D 138 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.108000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.087221 restraints weight = 5369.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.00
r_work: 0.3225 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4656  Z= 0.186
  Angle     :  0.633   9.764   6352  Z= 0.334
  Chirality :  0.051   0.128    800
  Planarity :  0.003   0.017    760
  Dihedral  :  6.472  28.611    932
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 17.06 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.34 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 140 
 TYR   0.015   0.002   TYR A 143 
 PHE   0.018   0.003   PHE C 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 4640)
  covalent geometry    : angle       0.62093 ( 6308)
  SS BOND              : bond        0.00110 (    4)
  SS BOND              : angle       0.53720 (    8)
  hydrogen bonds       : bond        0.02723 (  109)
  hydrogen bonds       : angle       5.56252 (  327)
  link_NAG-ASN         : bond        0.00102 (   12)
  link_NAG-ASN         : angle       1.73924 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  144 LEU cc_start: 0.8916 (tt) cc_final: 0.8712 (tt)
REVERT: B  178 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8151 (mtpt)
REVERT: B  192 MET cc_start: 0.8362 (mtp) cc_final: 0.8030 (mtm)
REVERT: A  192 MET cc_start: 0.8621 (mtp) cc_final: 0.8416 (mtp)
REVERT: C  192 MET cc_start: 0.8472 (mtp) cc_final: 0.8258 (mtm)
REVERT: D  139 LYS cc_start: 0.8218 (ttmt) cc_final: 0.6912 (tppt)
REVERT: D  192 MET cc_start: 0.8661 (mtp) cc_final: 0.8357 (mtm)
REVERT: D  209 TYR cc_start: 0.7991 (m-80) cc_final: 0.7600 (m-80)
  outliers start: 7
  outliers final: 0
  residues processed: 117
  average time/residue: 0.6842
  time to fit residues: 82.0843
Evaluate side-chains
  113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 18 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
B 194 GLN
A 138 GLN
A 229 GLN
C 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.109188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.088222 restraints weight = 5398.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.02
r_work: 0.3242 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8903
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   4656  Z= 0.158
  Angle     :  0.614  10.408   6352  Z= 0.324
  Chirality :  0.051   0.126    800
  Planarity :  0.002   0.018    760
  Dihedral  :  6.288  28.267    932
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 17.86 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.34 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 140 
 TYR   0.014   0.002   TYR A 143 
 PHE   0.017   0.003   PHE C 213 
 HIS   0.005   0.002   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4640)
  covalent geometry    : angle       0.60290 ( 6308)
  SS BOND              : bond        0.00091 (    4)
  SS BOND              : angle       0.46965 (    8)
  hydrogen bonds       : bond        0.02508 (  109)
  hydrogen bonds       : angle       5.47504 (  327)
  link_NAG-ASN         : bond        0.00082 (   12)
  link_NAG-ASN         : angle       1.69078 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.9080 (mttt) cc_final: 0.8788 (mttt)
REVERT: B  178 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8099 (mtpt)
REVERT: B  192 MET cc_start: 0.8352 (mtp) cc_final: 0.7980 (mtm)
REVERT: D  139 LYS cc_start: 0.8122 (ttmt) cc_final: 0.6876 (tppt)
REVERT: D  192 MET cc_start: 0.8658 (mtp) cc_final: 0.8343 (mtm)
REVERT: D  209 TYR cc_start: 0.7937 (m-80) cc_final: 0.7585 (m-80)
  outliers start: 4
  outliers final: 0
  residues processed: 114
  average time/residue: 0.6906
  time to fit residues: 80.8977
Evaluate side-chains
  111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
C 138 GLN
C 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.106384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.085793 restraints weight = 5345.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.98
r_work: 0.3202 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   4656  Z= 0.262
  Angle     :  0.708  10.981   6352  Z= 0.373
  Chirality :  0.052   0.132    800
  Planarity :  0.003   0.027    760
  Dihedral  :  7.038  32.502    932
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 17.46 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 140 
 TYR   0.018   0.002   TYR B 143 
 PHE   0.020   0.003   PHE C 213 
 HIS   0.004   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 4640)
  covalent geometry    : angle       0.69630 ( 6308)
  SS BOND              : bond        0.00130 (    4)
  SS BOND              : angle       0.71392 (    8)
  hydrogen bonds       : bond        0.03157 (  109)
  hydrogen bonds       : angle       5.73706 (  327)
  link_NAG-ASN         : bond        0.00145 (   12)
  link_NAG-ASN         : angle       1.80478 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8189 (mtpt)
REVERT: B  192 MET cc_start: 0.8361 (mtp) cc_final: 0.7977 (mtm)
REVERT: B  193 LYS cc_start: 0.8637 (tttp) cc_final: 0.8357 (tptt)
REVERT: D  139 LYS cc_start: 0.8275 (ttmt) cc_final: 0.6915 (tppt)
REVERT: D  178 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8142 (mtpp)
REVERT: D  192 MET cc_start: 0.8686 (mtp) cc_final: 0.8392 (mtm)
REVERT: D  209 TYR cc_start: 0.8003 (m-80) cc_final: 0.7579 (m-80)
  outliers start: 7
  outliers final: 0
  residues processed: 121
  average time/residue: 0.6780
  time to fit residues: 84.3151
Evaluate side-chains
  117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0870
   chunk 22 optimal weight:    8.9990
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
A 229 GLN
C 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.109121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.088225 restraints weight = 5268.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.99
r_work: 0.3242 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8905
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4656  Z= 0.168
  Angle     :  0.640  11.407   6352  Z= 0.337
  Chirality :  0.051   0.127    800
  Planarity :  0.002   0.018    760
  Dihedral  :  6.611  30.823    932
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 18.45 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.015   0.002   TYR C 211 
 PHE   0.016   0.003   PHE C 213 
 HIS   0.005   0.002   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4640)
  covalent geometry    : angle       0.62959 ( 6308)
  SS BOND              : bond        0.00083 (    4)
  SS BOND              : angle       0.49974 (    8)
  hydrogen bonds       : bond        0.02564 (  109)
  hydrogen bonds       : angle       5.52739 (  327)
  link_NAG-ASN         : bond        0.00085 (   12)
  link_NAG-ASN         : angle       1.68522 (   36)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8111 (mtpt)
REVERT: B  192 MET cc_start: 0.8368 (mtp) cc_final: 0.7996 (mtm)
REVERT: B  193 LYS cc_start: 0.8577 (tttp) cc_final: 0.8375 (tptt)
REVERT: D  139 LYS cc_start: 0.8215 (ttmt) cc_final: 0.6873 (tppt)
REVERT: D  192 MET cc_start: 0.8655 (mtp) cc_final: 0.8330 (mtm)
REVERT: D  209 TYR cc_start: 0.7966 (m-80) cc_final: 0.7555 (m-80)
  outliers start: 4
  outliers final: 0
  residues processed: 113
  average time/residue: 0.6612
  time to fit residues: 76.7184
Evaluate side-chains
  111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 49 optimal weight:    0.4980
   chunk 8 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0040
   chunk 48 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    2.8998

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
A 229 GLN
C 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087496 restraints weight = 5373.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.03
r_work: 0.3227 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4656  Z= 0.184
  Angle     :  0.656  11.174   6352  Z= 0.346
  Chirality :  0.051   0.148    800
  Planarity :  0.003   0.019    760
  Dihedral  :  6.479  28.814    932
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 18.85 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.32), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.015   0.002   TYR B 143 
 PHE   0.017   0.003   PHE C 213 
 HIS   0.005   0.002   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 4640)
  covalent geometry    : angle       0.64568 ( 6308)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       0.54050 (    8)
  hydrogen bonds       : bond        0.02649 (  109)
  hydrogen bonds       : angle       5.55284 (  327)
  link_NAG-ASN         : bond        0.00103 (   12)
  link_NAG-ASN         : angle       1.68282 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2054.77 seconds
wall clock time: 35 minutes 43.42 seconds (2143.42 seconds total)