Starting phenix.real_space_refine
on Sat Aug 23 00:44:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6s_35205/08_2025/8i6s_35205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6s_35205/08_2025/8i6s_35205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6s_35205/08_2025/8i6s_35205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6s_35205/08_2025/8i6s_35205.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6s_35205/08_2025/8i6s_35205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6s_35205/08_2025/8i6s_35205.map"
  }
  resolution = 4.4
  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=  -0.002 sd=   0.032
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      20      5.16       5
     C    5581      2.51       5
     N    1432      2.21       5
     O    1600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  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: 8641
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2261
          Classifications: {'peptide': 301}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 20, 'GLN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 65
    Chain: "B"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 2316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2316
          Classifications: {'peptide': 303}
          Link IDs: {'PTRANS': 12, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 1679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1679
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 45
    Chain: "E"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 641
          Classifications: {'peptide': 77}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.45, per 1000 atoms: 0.28
  Number of scatterers: 8641
  At special positions: 0
  Unit cell: (66.066, 78.936, 179.322, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P       6     15.00
     Mg      2     11.99
     O    1600      8.00
     N    1432      7.00
     C    5581      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 358.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2050

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      56.5% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 54
    Processing helix  chain 'A' and resid 55 through 69
      removed outlier: 3.726A  pdb=" N   SER A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL A  65 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   THR A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 81
      removed outlier: 3.953A  pdb=" N   MET A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A  79 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
      removed outlier: 3.573A  pdb=" N   GLY A 109 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 114 " --> pdb=" O   GLN A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 142
      removed outlier: 3.644A  pdb=" N   ALA A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 178
      removed outlier: 3.715A  pdb=" N   ARG A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 231
      removed outlier: 3.541A  pdb=" N   ILE A 213 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   LEU A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 244
      removed outlier: 4.262A  pdb=" N   ILE A 238 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU A 239 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL A 244 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 293
      removed outlier: 3.547A  pdb=" N   ARG A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
      Proline residue:  A 254  - end of helix
      removed outlier: 3.651A  pdb=" N   TYR A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TYR A 262 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TRP A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   SER A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ASN A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LEU A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 332
      removed outlier: 3.508A  pdb=" N   THR A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU A 332 " --> pdb=" O   HIS A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 49
    Processing helix  chain 'B' and resid 73 through 80
      removed outlier: 3.925A  pdb=" N   LEU B  77 " --> pdb=" O   GLN B  73 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLN B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 3.858A  pdb=" N   ASN B  99 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 112
      No H-bonds generated for 'chain 'B' and resid 110 through 112'
    Processing helix  chain 'B' and resid 113 through 125
      removed outlier: 4.028A  pdb=" N   LEU B 122 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   GLU B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ARG B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.694A  pdb=" N   LEU B 138 " --> pdb=" O   PRO B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 153
      removed outlier: 4.120A  pdb=" N   GLN B 144 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 186
      removed outlier: 4.690A  pdb=" N   GLU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU B 181 " --> pdb=" O   MET B 177 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ASP B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU B 186 " --> pdb=" O   ASP B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 3.632A  pdb=" N   ALA B 201 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ARG B 202 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 198 through 202'
    Processing helix  chain 'C' and resid 34 through 54
    Processing helix  chain 'C' and resid 55 through 69
      removed outlier: 3.632A  pdb=" N   PHE C  60 " --> pdb=" O   PRO C  56 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS C  63 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL C  65 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR C  69 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 84
      removed outlier: 3.833A  pdb=" N   MET C  74 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU C  84 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.587A  pdb=" N   ARG C  92 " --> pdb=" O   SER C  89 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ALA C  93 " --> pdb=" O   TRP C  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 89 through 93'
    Processing helix  chain 'C' and resid 106 through 119
      removed outlier: 3.565A  pdb=" N   ASP C 111 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU C 117 " --> pdb=" O   ARG C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 139
      removed outlier: 3.912A  pdb=" N   LEU C 137 " --> pdb=" O   ALA C 133 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLN C 138 " --> pdb=" O   LEU C 134 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLU C 139 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 173
      removed outlier: 3.732A  pdb=" N   ALA C 173 " --> pdb=" O   GLY C 170 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 170 through 173'
    Processing helix  chain 'C' and resid 174 through 179
      removed outlier: 3.610A  pdb=" N   LEU C 178 " --> pdb=" O   LEU C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 196
      removed outlier: 4.722A  pdb=" N   GLU C 195 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG C 196 " --> pdb=" O   VAL C 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 191 through 196'
    Processing helix  chain 'C' and resid 196 through 201
    Processing helix  chain 'C' and resid 202 through 233
      removed outlier: 3.536A  pdb=" N   ILE C 213 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   VAL C 216 " --> pdb=" O   THR C 212 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU C 221 " --> pdb=" O   LEU C 217 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL C 222 " --> pdb=" O   THR C 218 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ARG C 228 " --> pdb=" O   GLY C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 4.510A  pdb=" N   GLU C 239 " --> pdb=" O   ARG C 235 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL C 240 " --> pdb=" O   ASN C 236 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE C 241 " --> pdb=" O   GLU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 292
      removed outlier: 3.712A  pdb=" N   VAL C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      Proline residue:  C 254  - end of helix
      removed outlier: 3.684A  pdb=" N   TYR C 257 " --> pdb=" O   ARG C 253 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   MET C 258 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TYR C 262 " --> pdb=" O   MET C 258 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE C 268 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU C 273 " --> pdb=" O   LEU C 269 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   GLY C 283 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   SER C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 332
      removed outlier: 3.869A  pdb=" N   ALA C 326 " --> pdb=" O   TRP C 322 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ARG C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   HIS C 328 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 50
      removed outlier: 3.661A  pdb=" N   ILE D  48 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU D  49 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 80
      removed outlier: 3.927A  pdb=" N   LEU D  77 " --> pdb=" O   GLN D  73 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLN D  80 " --> pdb=" O   PHE D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 101
    Processing helix  chain 'D' and resid 101 through 108
      removed outlier: 3.742A  pdb=" N   GLN D 105 " --> pdb=" O   ALA D 101 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE D 106 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 112
      No H-bonds generated for 'chain 'D' and resid 110 through 112'
    Processing helix  chain 'D' and resid 113 through 122
      removed outlier: 3.574A  pdb=" N   ARG D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL D 118 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 153
      removed outlier: 4.027A  pdb=" N   ARG D 145 " --> pdb=" O   GLY D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 183
      removed outlier: 3.957A  pdb=" N   SER D 174 " --> pdb=" O   PRO D 170 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU D 175 " --> pdb=" O   ARG D 171 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLU D 181 " --> pdb=" O   MET D 177 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP D 182 " --> pdb=" O   GLY D 178 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 114
      removed outlier: 3.612A  pdb=" N   GLN E  96 " --> pdb=" O   LYS E  92 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ALA E  98 " --> pdb=" O   LYS E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 136 through 163
      removed outlier: 3.507A  pdb=" N   ARG E 148 " --> pdb=" O   ILE E 144 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU E 149 " --> pdb=" O   ASN E 145 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLU E 150 " --> pdb=" O   LYS E 146 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLN E 151 " --> pdb=" O   ALA E 147 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR E 158 " --> pdb=" O   SER E 154 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG E 160 " --> pdb=" O   ASN E 156 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN E 161 " --> pdb=" O   GLU E 157 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127
    Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 25
      removed outlier: 6.829A  pdb=" N   VAL B  21 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLN B   6 " --> pdb=" O   VAL B  21 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE B   4 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33
      removed outlier: 6.118A  pdb=" N   PHE B  32 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 61
      removed outlier: 4.468A  pdb=" N   LEU B  59 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LEU B  61 " --> pdb=" O   GLN B  64 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLN B  64 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 159
    Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 128
      removed outlier: 4.181A  pdb=" N   GLN C 126 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE C 128 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL C 158 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5
      removed outlier: 4.016A  pdb=" N   GLU D   5 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS D  58 " --> pdb=" O   GLU D   5 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU D  61 " --> pdb=" O   GLN D  64 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN D  64 " --> pdb=" O   LEU D  61 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 190 through 193
      removed outlier: 3.882A  pdb=" N   VAL D  33 " --> pdb=" O   ILE D 192 " (cutoff:3.500A)
      removed outlier: 8.340A  pdb=" N   LEU D 208 " --> pdb=" O   ILE D  30 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   PHE D  32 " --> pdb=" O   LEU D 208 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   LEU D 210 " --> pdb=" O   PHE D  32 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   THR D  34 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 81 through 82
      removed outlier: 3.611A  pdb=" N   GLY D  82 " --> pdb=" O   LEU D 158 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    361 hydrogen bonds defined for protein.
    1071 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2048
        1.33 -     1.46: 1723
        1.46 -     1.58: 4967
        1.58 -     1.70: 10
        1.70 -     1.83: 38
  Bond restraints: 8786
  Sorted by residual:
  bond pdb=" C6  ATP D 301 "
       pdb=" N6  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.449 -0.112 1.10e-02 8.26e+03 1.04e+02
  bond pdb=" C6  ATP B 302 "
       pdb=" N6  ATP B 302 "
    ideal  model  delta    sigma   weight residual
    1.337  1.449 -0.112 1.10e-02 8.26e+03 1.03e+02
  bond pdb=" C5  ATP B 302 "
       pdb=" N7  ATP B 302 "
    ideal  model  delta    sigma   weight residual
    1.387  1.469 -0.082 1.00e-02 1.00e+04 6.69e+01
  bond pdb=" C5  ATP D 301 "
       pdb=" N7  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.387  1.468 -0.081 1.00e-02 1.00e+04 6.57e+01
  bond pdb=" O5' ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.579  1.650 -0.071 1.10e-02 8.26e+03 4.14e+01
  ... (remaining 8781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.67: 11671
        4.67 -     9.34: 180
        9.34 -    14.01: 29
       14.01 -    18.68: 5
       18.68 -    23.35: 1
  Bond angle restraints: 11886
  Sorted by residual:
  angle pdb=" PB  ATP B 302 "
        pdb=" O3B ATP B 302 "
        pdb=" PG  ATP B 302 "
      ideal   model   delta    sigma   weight residual
     139.87  116.52   23.35 1.00e+00 1.00e+00 5.45e+02
  angle pdb=" PB  ATP D 301 "
        pdb=" O3B ATP D 301 "
        pdb=" PG  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     139.87  125.37   14.50 1.00e+00 1.00e+00 2.10e+02
  angle pdb=" PA  ATP B 302 "
        pdb=" O3A ATP B 302 "
        pdb=" PB  ATP B 302 "
      ideal   model   delta    sigma   weight residual
     136.83  122.76   14.07 1.00e+00 1.00e+00 1.98e+02
  angle pdb=" O3A ATP B 302 "
        pdb=" PB  ATP B 302 "
        pdb=" O3B ATP B 302 "
      ideal   model   delta    sigma   weight residual
     101.57  116.72  -15.15 1.54e+00 4.24e-01 9.73e+01
  angle pdb=" PA  ATP D 301 "
        pdb=" O3A ATP D 301 "
        pdb=" PB  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     136.83  127.43    9.40 1.00e+00 1.00e+00 8.84e+01
  ... (remaining 11881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4659
       17.97 -    35.95: 550
       35.95 -    53.92: 125
       53.92 -    71.89: 23
       71.89 -    89.86: 9
  Dihedral angle restraints: 5366
    sinusoidal: 2178
      harmonic: 3188
  Sorted by residual:
  dihedral pdb=" CA  VAL A 192 "
           pdb=" C   VAL A 192 "
           pdb=" N   TRP A 193 "
           pdb=" CA  TRP A 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.38   42.62     0      5.00e+00 4.00e-02 7.27e+01
  dihedral pdb=" CA  ASP C 190 "
           pdb=" C   ASP C 190 "
           pdb=" N   LEU C 191 "
           pdb=" CA  LEU C 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.62  -22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  LEU A 229 "
           pdb=" C   LEU A 229 "
           pdb=" N   HIS A 230 "
           pdb=" CA  HIS A 230 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.90   22.10     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 5363 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1133
       0.073 -    0.146: 224
       0.146 -    0.219: 46
       0.219 -    0.292: 5
       0.292 -    0.365: 3
  Chirality restraints: 1411
  Sorted by residual:
  chirality pdb=" CB  ILE B 215 "
            pdb=" CA  ILE B 215 "
            pdb=" CG1 ILE B 215 "
            pdb=" CG2 ILE B 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CB  ILE D   2 "
            pdb=" CA  ILE D   2 "
            pdb=" CG1 ILE D   2 "
            pdb=" CG2 ILE D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CB  VAL B 125 "
            pdb=" CA  VAL B 125 "
            pdb=" CG1 VAL B 125 "
            pdb=" CG2 VAL B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.18e+00
  ... (remaining 1408 not shown)

  Planarity restraints: 1476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 195 "   -0.045 2.00e-02 2.50e+03   6.17e-02 5.71e+01
        pdb=" CG  HIS B 195 "    0.107 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 195 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 195 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 195 "    0.050 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 195 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 192 "   -0.025 2.00e-02 2.50e+03   4.92e-02 2.42e+01
        pdb=" C   VAL A 192 "    0.085 2.00e-02 2.50e+03
        pdb=" O   VAL A 192 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   TRP A 193 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 280 "   -0.013 2.00e-02 2.50e+03   1.55e-02 6.01e+00
        pdb=" CG  TRP C 280 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 280 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 280 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 280 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 280 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 280 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 280 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 280 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 280 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1473 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 84
        2.64 -     3.20: 7059
        3.20 -     3.77: 13820
        3.77 -     4.33: 17569
        4.33 -     4.90: 27254
  Nonbonded interactions: 65786
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 140 "
            pdb="MG    MG B 301 "
     model   vdw
     2.073 2.170
  nonbonded pdb="MG    MG B 301 "
            pdb=" O3A ATP D 301 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" O1A ATP B 302 "
            pdb="MG    MG B 303 "
     model   vdw
     2.133 2.170
  nonbonded pdb="MG    MG B 301 "
            pdb=" O2B ATP D 301 "
     model   vdw
     2.135 2.170
  nonbonded pdb=" O1B ATP B 302 "
            pdb="MG    MG B 303 "
     model   vdw
     2.253 2.170
  ... (remaining 65781 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and (resid 35 through 88 or (resid 89 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 90 or (resid 91 through 95 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 96 through 122 or (resid 123 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 124 through 164 o \ 
r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 
66 or (resid 167 through 169 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 170 or (resid 171 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 172 through 194 or (resid 195 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 196 or (resid 197 through 199 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 200 through 335))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ 
 or name CZ )) or resid 12 through 222))
  selection = (chain 'D' and resid 1 through 222)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.960
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6010
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      :  0.006   0.112   8787  Z= 0.413
  Angle     :  1.394  23.352  11886  Z= 0.763
  Chirality :  0.063   0.365   1411
  Planarity :  0.007   0.062   1476
  Dihedral  : 16.404  89.863   3316
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.13 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  2.48 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -5.18 (0.17), residues: 1115
  helix: -4.23 (0.09), residues: 575
  sheet: -0.91 (0.68), residues: 55
  loop : -2.52 (0.22), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 118 
 TYR   0.040   0.002   TYR A 250 
 PHE   0.039   0.001   PHE D 180 
 TRP   0.041   0.002   TRP C 280 
 HIS   0.080   0.004   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 8786)
  covalent geometry    : angle       1.39357 (11886)
  hydrogen bonds       : bond        0.31506 (  361)
  hydrogen bonds       : angle      10.18497 ( 1071)
  Misc. bond           : bond        0.01761 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.6692 (mmp) cc_final: 0.6455 (mmp)
REVERT: A  215 LEU cc_start: 0.6983 (mm) cc_final: 0.5502 (tp)
REVERT: B  162 ASP cc_start: 0.7197 (p0) cc_final: 0.6968 (p0)
REVERT: C   66 MET cc_start: 0.4364 (tpt) cc_final: 0.3997 (tpt)
REVERT: D  154 HIS cc_start: 0.6844 (p-80) cc_final: 0.5443 (t-90)
  outliers start: 9
  outliers final: 9
  residues processed: 126
  average time/residue: 0.0732
  time to fit residues: 13.9328
Evaluate side-chains
  85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0170
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0060
   chunk 106 optimal weight:    4.9990
   overall best weight:    0.4634

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
A 230 HIS
C  82 ASN
E 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.097990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.080786 restraints weight = 53477.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.082543 restraints weight = 37925.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.083802 restraints weight = 29636.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.084708 restraints weight = 24761.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.085343 restraints weight = 21762.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6115
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8787  Z= 0.121
  Angle     :  0.642   7.008  11886  Z= 0.324
  Chirality :  0.041   0.186   1411
  Planarity :  0.004   0.034   1476
  Dihedral  :  8.343  71.649   1213
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.14 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  5.40 %
    Favored  : 93.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.61 (0.22), residues: 1115
  helix: -1.50 (0.18), residues: 581
  sheet: -0.88 (0.70), residues: 53
  loop : -2.00 (0.25), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 148 
 TYR   0.007   0.001   TYR A 250 
 PHE   0.011   0.001   PHE C 207 
 TRP   0.014   0.002   TRP A 271 
 HIS   0.021   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8786)
  covalent geometry    : angle       0.64173 (11886)
  hydrogen bonds       : bond        0.05256 (  361)
  hydrogen bonds       : angle       4.82804 ( 1071)
  Misc. bond           : bond        0.00488 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9204 (tt) cc_final: 0.8927 (pp)
REVERT: A  230 HIS cc_start: 0.5546 (OUTLIER) cc_final: 0.5294 (t70)
REVERT: B  162 ASP cc_start: 0.7283 (p0) cc_final: 0.6804 (p0)
REVERT: C  295 ASP cc_start: 0.8103 (p0) cc_final: 0.7858 (p0)
  outliers start: 10
  outliers final: 8
  residues processed: 115
  average time/residue: 0.0739
  time to fit residues: 13.0755
Evaluate side-chains
  85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    0.3980
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN
C 188 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.093742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.076931 restraints weight = 54968.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.078472 restraints weight = 39988.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.079608 restraints weight = 31879.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.080408 restraints weight = 27046.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.081003 restraints weight = 23863.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6291
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8787  Z= 0.145
  Angle     :  0.661   6.969  11886  Z= 0.332
  Chirality :  0.042   0.150   1411
  Planarity :  0.004   0.033   1476
  Dihedral  :  8.010  70.192   1213
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.59 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.34 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.44 (0.24), residues: 1115
  helix: -0.25 (0.21), residues: 588
  sheet: -1.38 (0.64), residues: 55
  loop : -1.75 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 104 
 TYR   0.010   0.002   TYR E 141 
 PHE   0.011   0.001   PHE C 255 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.021   0.002   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8786)
  covalent geometry    : angle       0.66100 (11886)
  hydrogen bonds       : bond        0.04680 (  361)
  hydrogen bonds       : angle       4.40649 ( 1071)
  Misc. bond           : bond        0.00385 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9313 (tt) cc_final: 0.9061 (pp)
REVERT: B  162 ASP cc_start: 0.7363 (p0) cc_final: 0.6770 (p0)
REVERT: C  295 ASP cc_start: 0.8114 (p0) cc_final: 0.7877 (p0)
REVERT: D  180 PHE cc_start: 0.9081 (m-10) cc_final: 0.8717 (m-80)
  outliers start: 8
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0717
  time to fit residues: 11.0054
Evaluate side-chains
  80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 HIS
** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.094846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.077752 restraints weight = 55556.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.079318 restraints weight = 40575.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.080468 restraints weight = 32450.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.081286 restraints weight = 27453.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.081895 restraints weight = 24292.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6252
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8787  Z= 0.112
  Angle     :  0.621   7.709  11886  Z= 0.302
  Chirality :  0.041   0.150   1411
  Planarity :  0.003   0.033   1476
  Dihedral  :  7.641  73.524   1213
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.41 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  5.94 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.25), residues: 1115
  helix:  0.36 (0.22), residues: 586
  sheet: -1.09 (0.68), residues: 53
  loop : -1.70 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 148 
 TYR   0.011   0.001   TYR C  37 
 PHE   0.009   0.001   PHE C 207 
 TRP   0.010   0.001   TRP A 271 
 HIS   0.020   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8786)
  covalent geometry    : angle       0.62057 (11886)
  hydrogen bonds       : bond        0.03824 (  361)
  hydrogen bonds       : angle       4.15436 ( 1071)
  Misc. bond           : bond        0.00387 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9303 (tt) cc_final: 0.9042 (pp)
REVERT: B  162 ASP cc_start: 0.7454 (p0) cc_final: 0.6862 (p0)
REVERT: C  295 ASP cc_start: 0.8075 (p0) cc_final: 0.7729 (p0)
REVERT: D  180 PHE cc_start: 0.8961 (m-10) cc_final: 0.8639 (m-80)
  outliers start: 8
  outliers final: 8
  residues processed: 103
  average time/residue: 0.0740
  time to fit residues: 11.5970
Evaluate side-chains
  84 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0870
   chunk 90 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
A 282 ASN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 HIS
** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.094516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.077904 restraints weight = 54841.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.079390 restraints weight = 40305.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.080461 restraints weight = 32325.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.081207 restraints weight = 27555.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.081527 restraints weight = 24620.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6262
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8787  Z= 0.113
  Angle     :  0.620   8.406  11886  Z= 0.302
  Chirality :  0.041   0.156   1411
  Planarity :  0.003   0.031   1476
  Dihedral  :  7.209  77.089   1213
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  5.18 %
    Favored  : 93.74 %
  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: -0.58 (0.25), residues: 1115
  helix:  0.62 (0.22), residues: 586
  sheet: -1.39 (0.63), residues: 63
  loop : -1.52 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 148 
 TYR   0.010   0.001   TYR C  37 
 PHE   0.007   0.001   PHE C 207 
 TRP   0.009   0.001   TRP A 271 
 HIS   0.023   0.002   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8786)
  covalent geometry    : angle       0.61957 (11886)
  hydrogen bonds       : bond        0.03661 (  361)
  hydrogen bonds       : angle       4.07092 ( 1071)
  Misc. bond           : bond        0.00459 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9322 (tt) cc_final: 0.9064 (pp)
REVERT: B  159 LEU cc_start: 0.8496 (tp) cc_final: 0.8292 (tt)
REVERT: B  162 ASP cc_start: 0.7387 (p0) cc_final: 0.6825 (p0)
REVERT: C   82 ASN cc_start: 0.4065 (OUTLIER) cc_final: 0.3823 (t0)
REVERT: C  295 ASP cc_start: 0.8147 (p0) cc_final: 0.7789 (p0)
REVERT: D  180 PHE cc_start: 0.9022 (m-10) cc_final: 0.8639 (m-80)
  outliers start: 10
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0723
  time to fit residues: 11.7258
Evaluate side-chains
  87 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:    0.0170
   chunk 81 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 99 optimal weight:    0.1980
   chunk 102 optimal weight:    0.2980
   chunk 107 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0570
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN
C 233 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.095784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.079099 restraints weight = 54037.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.080722 restraints weight = 39406.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.081871 restraints weight = 31330.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.082735 restraints weight = 26446.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.083327 restraints weight = 23310.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8787  Z= 0.103
  Angle     :  0.622   7.973  11886  Z= 0.298
  Chirality :  0.041   0.167   1411
  Planarity :  0.003   0.031   1476
  Dihedral  :  6.970  72.764   1213
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.41 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  4.21 %
    Favored  : 94.71 %
  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: -0.36 (0.26), residues: 1115
  helix:  0.83 (0.22), residues: 585
  sheet: -1.07 (0.69), residues: 53
  loop : -1.49 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 148 
 TYR   0.010   0.001   TYR C  37 
 PHE   0.025   0.001   PHE C  53 
 TRP   0.010   0.001   TRP A 271 
 HIS   0.014   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 8786)
  covalent geometry    : angle       0.62183 (11886)
  hydrogen bonds       : bond        0.03324 (  361)
  hydrogen bonds       : angle       3.93793 ( 1071)
  Misc. bond           : bond        0.00303 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9317 (tt) cc_final: 0.9060 (pp)
REVERT: B  159 LEU cc_start: 0.8533 (tp) cc_final: 0.8314 (tt)
REVERT: B  162 ASP cc_start: 0.7352 (p0) cc_final: 0.6817 (p0)
REVERT: C   53 PHE cc_start: 0.7470 (m-80) cc_final: 0.7245 (m-80)
REVERT: C  295 ASP cc_start: 0.8172 (p0) cc_final: 0.7820 (p0)
REVERT: D  180 PHE cc_start: 0.8972 (m-10) cc_final: 0.8630 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0742
  time to fit residues: 12.3915
Evaluate side-chains
  85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0020
   chunk 23 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 103 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 167 ASN
C  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.095301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.078240 restraints weight = 55038.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.079795 restraints weight = 40668.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.080933 restraints weight = 32624.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.081743 restraints weight = 27689.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.082328 restraints weight = 24606.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6220
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8787  Z= 0.108
  Angle     :  0.626   8.071  11886  Z= 0.301
  Chirality :  0.042   0.162   1411
  Planarity :  0.003   0.041   1476
  Dihedral  :  6.973  75.549   1213
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.48 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  4.00 %
    Favored  : 94.92 %
  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: -0.19 (0.26), residues: 1115
  helix:  0.98 (0.23), residues: 586
  sheet: -1.32 (0.64), residues: 63
  loop : -1.39 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  99 
 TYR   0.010   0.001   TYR C  37 
 PHE   0.024   0.001   PHE C  53 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.027   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8786)
  covalent geometry    : angle       0.62633 (11886)
  hydrogen bonds       : bond        0.03320 (  361)
  hydrogen bonds       : angle       3.91290 ( 1071)
  Misc. bond           : bond        0.00602 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  162 ASP cc_start: 0.7354 (p0) cc_final: 0.6788 (p0)
REVERT: C   53 PHE cc_start: 0.7464 (m-80) cc_final: 0.7158 (m-80)
REVERT: C  295 ASP cc_start: 0.8128 (p0) cc_final: 0.7760 (p0)
REVERT: D  180 PHE cc_start: 0.8983 (m-10) cc_final: 0.8626 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0694
  time to fit residues: 11.6771
Evaluate side-chains
  86 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    0.0470
   chunk 12 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0570
   chunk 72 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 86 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.096323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.079348 restraints weight = 54587.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.080920 restraints weight = 40219.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.082093 restraints weight = 32215.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.082949 restraints weight = 27289.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.083559 restraints weight = 24121.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6169
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8787  Z= 0.103
  Angle     :  0.643   7.984  11886  Z= 0.304
  Chirality :  0.042   0.151   1411
  Planarity :  0.003   0.031   1476
  Dihedral  :  6.867  76.378   1213
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.77 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  2.81 %
    Favored  : 96.11 %
  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: -0.05 (0.26), residues: 1115
  helix:  1.12 (0.23), residues: 586
  sheet: -1.22 (0.65), residues: 63
  loop : -1.36 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.009   0.001   TYR C  37 
 PHE   0.022   0.001   PHE C  53 
 TRP   0.009   0.001   TRP A 271 
 HIS   0.019   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8786)
  covalent geometry    : angle       0.64287 (11886)
  hydrogen bonds       : bond        0.03095 (  361)
  hydrogen bonds       : angle       3.86636 ( 1071)
  Misc. bond           : bond        0.00366 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.360 
Fit side-chains
REVERT: C   53 PHE cc_start: 0.7436 (m-80) cc_final: 0.7150 (m-80)
REVERT: C  295 ASP cc_start: 0.8088 (p0) cc_final: 0.7728 (p0)
REVERT: D  180 PHE cc_start: 0.8916 (m-10) cc_final: 0.8674 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0714
  time to fit residues: 11.9501
Evaluate side-chains
  85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
A 188 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.094765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.077726 restraints weight = 54151.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.079196 restraints weight = 40545.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.080285 restraints weight = 32739.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.081081 restraints weight = 27940.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.081650 restraints weight = 24925.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6247
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8787  Z= 0.113
  Angle     :  0.646   8.462  11886  Z= 0.309
  Chirality :  0.042   0.158   1411
  Planarity :  0.003   0.030   1476
  Dihedral  :  6.934  81.510   1213
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.22 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  2.81 %
    Favored  : 96.11 %
  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: -0.05 (0.26), residues: 1115
  helix:  1.13 (0.23), residues: 588
  sheet: -1.28 (0.62), residues: 70
  loop : -1.38 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.010   0.001   TYR C  37 
 PHE   0.021   0.001   PHE C  53 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.016   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8786)
  covalent geometry    : angle       0.64556 (11886)
  hydrogen bonds       : bond        0.03246 (  361)
  hydrogen bonds       : angle       3.84674 ( 1071)
  Misc. bond           : bond        0.00381 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   38 LEU cc_start: 0.8092 (tp) cc_final: 0.7817 (tp)
REVERT: C   53 PHE cc_start: 0.7634 (m-80) cc_final: 0.7319 (m-80)
REVERT: C  295 ASP cc_start: 0.8075 (p0) cc_final: 0.7692 (p0)
REVERT: D  180 PHE cc_start: 0.8973 (m-10) cc_final: 0.8674 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0714
  time to fit residues: 11.8714
Evaluate side-chains
  88 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 68 optimal weight:    0.0670
   chunk 102 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0040
   chunk 103 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.3730

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 HIS
C  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.095740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.078939 restraints weight = 53991.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.080521 restraints weight = 39863.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.081714 restraints weight = 31777.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.082559 restraints weight = 26867.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.083150 restraints weight = 23786.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6176
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8787  Z= 0.105
  Angle     :  0.655   8.669  11886  Z= 0.308
  Chirality :  0.042   0.161   1411
  Planarity :  0.003   0.031   1476
  Dihedral  :  6.852  77.938   1213
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  2.16 %
    Favored  : 96.76 %
  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:  0.05 (0.26), residues: 1115
  helix:  1.22 (0.23), residues: 587
  sheet: -1.29 (0.62), residues: 70
  loop : -1.33 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.009   0.001   TYR C  37 
 PHE   0.021   0.001   PHE C  53 
 TRP   0.010   0.001   TRP A 271 
 HIS   0.014   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8786)
  covalent geometry    : angle       0.65548 (11886)
  hydrogen bonds       : bond        0.03020 (  361)
  hydrogen bonds       : angle       3.77832 ( 1071)
  Misc. bond           : bond        0.00266 (    1)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.371 
Fit side-chains
REVERT: C   38 LEU cc_start: 0.8058 (tp) cc_final: 0.7795 (tp)
REVERT: C   53 PHE cc_start: 0.7510 (m-80) cc_final: 0.7229 (m-80)
REVERT: C  295 ASP cc_start: 0.8008 (p0) cc_final: 0.7631 (p0)
REVERT: D  180 PHE cc_start: 0.8873 (m-10) cc_final: 0.8620 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0682
  time to fit residues: 11.6544
Evaluate side-chains
  88 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 97 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0970
   chunk 27 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0770
   chunk 44 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.095553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.078875 restraints weight = 54059.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.080314 restraints weight = 40029.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.081369 restraints weight = 32264.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.082181 restraints weight = 27529.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.082752 restraints weight = 24430.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6195
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8787  Z= 0.104
  Angle     :  0.647   8.574  11886  Z= 0.305
  Chirality :  0.042   0.160   1411
  Planarity :  0.003   0.031   1476
  Dihedral  :  6.819  78.836   1213
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.13 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  2.16 %
    Favored  : 96.76 %
  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:  0.10 (0.26), residues: 1115
  helix:  1.27 (0.23), residues: 587
  sheet: -1.34 (0.61), residues: 70
  loop : -1.31 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.010   0.001   TYR C  37 
 PHE   0.020   0.001   PHE C  53 
 TRP   0.009   0.001   TRP A 271 
 HIS   0.013   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8786)
  covalent geometry    : angle       0.64700 (11886)
  hydrogen bonds       : bond        0.02999 (  361)
  hydrogen bonds       : angle       3.75618 ( 1071)
  Misc. bond           : bond        0.00277 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1804.68 seconds
wall clock time: 31 minutes 57.84 seconds (1917.84 seconds total)