Starting phenix.real_space_refine
on Tue Mar  3 19:31:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cfn_30345/03_2026/7cfn_30345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cfn_30345/03_2026/7cfn_30345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2026/7cfn_30345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2026/7cfn_30345.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2026/7cfn_30345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2026/7cfn_30345.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5158      2.51       5
     N    1416      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8112
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1930
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 232, 1914
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
      Conformer: "B"
        Number of residues, atoms: 232, 1914
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
          bond proxies already assigned to first conformer: 1932
    Chain: "B"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2587
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2076
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 274, 2070
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 21, 'TRANS': 252}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 274, 2070
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 21, 'TRANS': 252}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 2121
    Chain: "R"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 111
          Unusual residues: {'CLR': 1, 'FX0': 2, 'PLM': 1}
          Classifications: {'undetermined': 4, 'water': 1}
          Link IDs: {None: 4}
  Time building chain proxies: 2.67, per 1000 atoms: 0.33
  Number of scatterers: 8112
  At special positions: 0
  Unit cell: (79.092, 115.596, 119.652, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1492      8.00
     N    1416      7.00
     C    5158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 155 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 455.9 milliseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 10 sheets defined
      42.9% alpha, 19.3% 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 9 through 39
      removed outlier: 3.571A  pdb=" N   ARG A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.553A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.569A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.501A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.276A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.753A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.704A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.621A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 6 through 23
      removed outlier: 4.037A  pdb=" N   ALA G  10 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.754A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.748A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 19 through 42
      removed outlier: 3.987A  pdb=" N   ALA R  31 " --> pdb=" O   LEU R  27 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASP R  42 " --> pdb=" O   GLY R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 47
      removed outlier: 3.900A  pdb=" N   ARG R  46 " --> pdb=" O   ASP R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 67
      removed outlier: 3.581A  pdb=" N   CYS R  52 " --> pdb=" O   PRO R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 71 through 75
      removed outlier: 3.903A  pdb=" N   TRP R  75 " --> pdb=" O   PRO R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 116
      removed outlier: 4.151A  pdb=" N   LEU R  87 " --> pdb=" O   TRP R  83 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL R  88 " --> pdb=" O   SER R  84 " (cutoff:3.500A)
      Proline residue:  R  92  - end of helix
    Processing helix  chain 'R' and resid 123 through 140
      removed outlier: 3.558A  pdb=" N   ALA R 127 " --> pdb=" O   SER R 123 " (cutoff:3.500A)
      Proline residue:  R 135  - end of helix
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 156 through 161
    Processing helix  chain 'R' and resid 162 through 173
    Processing helix  chain 'R' and resid 175 through 207
      removed outlier: 4.365A  pdb=" N   ALA R 181 " --> pdb=" O   ALA R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 236
      removed outlier: 3.797A  pdb=" N   ALA R 217 " --> pdb=" O   ALA R 213 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 236 through 252
      removed outlier: 3.785A  pdb=" N   TYR R 240 " --> pdb=" O   CYS R 236 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL R 241 " --> pdb=" O   TRP R 237 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU R 252 " --> pdb=" O   VAL R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 275
      removed outlier: 4.498A  pdb=" N   THR R 261 " --> pdb=" O   LEU R 257 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU R 262 " --> pdb=" O   GLY R 258 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER R 264 " --> pdb=" O   GLY R 260 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER R 272 " --> pdb=" O   LEU R 268 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ALA R 273 " --> pdb=" O   GLY R 269 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ALA R 274 " --> pdb=" O   SER R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 282
    Processing helix  chain 'R' and resid 284 through 289
      removed outlier: 3.842A  pdb=" N   THR R 288 " --> pdb=" O   ASP R 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.864A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.649A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.895A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.665A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.773A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.661A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.711A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.611A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.062A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.733A  pdb=" N   LEU N  81 " --> pdb=" O   LEU N  20 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.757A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1111 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: 1.12

  Time building geometry restraints manager: 0.89 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: 1954
        1.33 -     1.45: 1779
        1.45 -     1.58: 4492
        1.58 -     1.70: 1
        1.70 -     1.82: 63
  Bond restraints: 8289
  Sorted by residual:
  bond pdb=" C27 FX0 R 401 "
       pdb=" O04 FX0 R 401 "
    ideal  model  delta    sigma   weight residual
    1.251  1.359 -0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" C27 FX0 R 403 "
       pdb=" O04 FX0 R 403 "
    ideal  model  delta    sigma   weight residual
    1.251  1.358 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C   ALA R 289 "
       pdb=" N   PRO R 290 "
    ideal  model  delta    sigma   weight residual
    1.334  1.429 -0.095 2.34e-02 1.83e+03 1.65e+01
  bond pdb=" C   HIS A 387 "
       pdb=" O   HIS A 387 "
    ideal  model  delta    sigma   weight residual
    1.237  1.206  0.031 1.17e-02 7.31e+03 6.94e+00
  bond pdb=" C   LEU A 388 "
       pdb=" O   LEU A 388 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.029 1.17e-02 7.31e+03 6.09e+00
  ... (remaining 8284 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 10627
        1.95 -     3.91: 525
        3.91 -     5.86: 81
        5.86 -     7.82: 30
        7.82 -     9.77: 10
  Bond angle restraints: 11273
  Sorted by residual:
  angle pdb=" N   VAL R 170 "
        pdb=" CA  VAL R 170 "
        pdb=" C   VAL R 170 "
      ideal   model   delta    sigma   weight residual
     110.72  115.97   -5.25 1.01e+00 9.80e-01 2.71e+01
  angle pdb=" N   LEU R  90 "
        pdb=" CA  LEU R  90 "
        pdb=" C   LEU R  90 "
      ideal   model   delta    sigma   weight residual
     111.69  117.96   -6.27 1.23e+00 6.61e-01 2.60e+01
  angle pdb=" N   GLU A 392 "
        pdb=" CA  GLU A 392 "
        pdb=" C   GLU A 392 "
      ideal   model   delta    sigma   weight residual
     110.80  118.87   -8.07 2.13e+00 2.20e-01 1.43e+01
  angle pdb=" C   ASP B  66 "
        pdb=" N   SER B  67 "
        pdb=" CA  SER B  67 "
      ideal   model   delta    sigma   weight residual
     123.47  129.26   -5.79 1.53e+00 4.27e-01 1.43e+01
  angle pdb=" CA  ALA R  91 "
        pdb=" C   ALA R  91 "
        pdb=" N   PRO R  92 "
      ideal   model   delta    sigma   weight residual
     120.93  117.35    3.58 1.06e+00 8.90e-01 1.14e+01
  ... (remaining 11268 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.71: 4796
       14.71 -    29.42: 238
       29.42 -    44.13: 75
       44.13 -    58.83: 16
       58.83 -    73.54: 10
  Dihedral angle restraints: 5135
    sinusoidal: 2146
      harmonic: 2989
  Sorted by residual:
  dihedral pdb=" CA  ASP A 331 "
           pdb=" C   ASP A 331 "
           pdb=" N   PRO A 332 "
           pdb=" CA  PRO A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.57  -26.43     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  ASP B 195 "
           pdb=" C   ASP B 195 "
           pdb=" N   THR B 196 "
           pdb=" CA  THR B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.36  -23.64     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.84   23.16     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 5132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1031
       0.077 -    0.154: 215
       0.154 -    0.231: 28
       0.231 -    0.308: 6
       0.308 -    0.385: 2
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" CA  GLU A 392 "
            pdb=" N   GLU A 392 "
            pdb=" C   GLU A 392 "
            pdb=" CB  GLU A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.70e+00
  chirality pdb=" CA  LEU R  90 "
            pdb=" N   LEU R  90 "
            pdb=" C   LEU R  90 "
            pdb=" CB  LEU R  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.76e+00
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.24e+00
  ... (remaining 1279 not shown)

  Planarity restraints: 1433
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "   -0.049 5.00e-02 4.00e+02   7.42e-02 8.81e+00
        pdb=" N   PRO N  88 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 289 "   -0.042 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO R 290 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO R 290 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO R 290 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "   -0.024 2.00e-02 2.50e+03   1.60e-02 6.36e+00
        pdb=" CG  TRP A 281 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1430 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 48
        2.56 -     3.15: 6006
        3.15 -     3.73: 12132
        3.73 -     4.32: 16769
        4.32 -     4.90: 28921
  Nonbonded interactions: 63876
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 394 "
            pdb=" OXT LEU A 394 "
     model   vdw
     1.979 3.460
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ARG B  22 "
            pdb=" NE2 GLN B 259 "
     model   vdw
     2.337 3.120
  ... (remaining 63871 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.810
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
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      :  0.008   0.108   8292  Z= 0.332
  Angle     :  1.039   9.772  11279  Z= 0.543
  Chirality :  0.064   0.385   1282
  Planarity :  0.007   0.074   1433
  Dihedral  : 10.747  73.543   3200
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.31 %
    Favored  : 96.57 %
  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 are not related in a simple way.
  whole: -2.77 (0.22), residues: 1020
  helix: -1.41 (0.21), residues: 398
  sheet: -1.88 (0.31), residues: 236
  loop : -2.04 (0.26), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 342 
 TYR   0.021   0.003   TYR A 339 
 PHE   0.026   0.003   PHE B 151 
 TRP   0.040   0.004   TRP A 281 
 HIS   0.013   0.003   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 ( 8289)
  covalent geometry    : angle       1.03880 (11273)
  SS BOND              : bond        0.00535 (    3)
  SS BOND              : angle       0.89410 (    6)
  hydrogen bonds       : bond        0.19234 (  386)
  hydrogen bonds       : angle       6.97273 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ASP cc_start: 0.7813 (m-30) cc_final: 0.7568 (m-30)
REVERT: A   35 GLN cc_start: 0.7176 (mt0) cc_final: 0.6666 (mp10)
REVERT: A   40 THR cc_start: 0.8881 (t) cc_final: 0.8556 (m)
REVERT: A   60 MET cc_start: 0.4235 (ptt) cc_final: 0.3658 (pmt)
REVERT: A  284 ASP cc_start: 0.8170 (m-30) cc_final: 0.7847 (m-30)
REVERT: B  155 ASN cc_start: 0.7960 (t0) cc_final: 0.7641 (t0)
REVERT: B  186 ASP cc_start: 0.7886 (p0) cc_final: 0.7593 (p0)
REVERT: B  323 ASP cc_start: 0.7911 (m-30) cc_final: 0.7587 (m-30)
REVERT: G   21 MET cc_start: 0.7013 (ttt) cc_final: 0.6603 (ttm)
REVERT: R  116 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7848 (mtt-85)
REVERT: R  204 ARG cc_start: 0.6992 (ttt90) cc_final: 0.6508 (ttm110)
REVERT: R  254 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.6946 (ptt180)
REVERT: R  268 LEU cc_start: 0.8111 (tt) cc_final: 0.7754 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 173
  average time/residue: 0.5905
  time to fit residues: 107.5995
Evaluate side-chains
  111 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 213 GLN
A 371 ASN
B  44 GLN
B 237 ASN
B 295 ASN
B 340 ASN
R  93 ASN
** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.156973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.120138 restraints weight = 24086.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 5.36
r_work: 0.3023 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8292  Z= 0.121
  Angle     :  0.637  12.452  11279  Z= 0.305
  Chirality :  0.043   0.270   1282
  Planarity :  0.004   0.049   1433
  Dihedral  :  6.019  51.912   1378
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.19 %
    Favored  : 84.97 %
  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 are not related in a simple way.
  whole: -0.75 (0.25), residues: 1020
  helix:  0.89 (0.25), residues: 394
  sheet: -1.24 (0.33), residues: 225
  loop : -1.37 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.020   0.001   TYR R 251 
 PHE   0.010   0.001   PHE A 212 
 TRP   0.021   0.002   TRP R 149 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8289)
  covalent geometry    : angle       0.63729 (11273)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       0.86265 (    6)
  hydrogen bonds       : bond        0.04535 (  386)
  hydrogen bonds       : angle       4.69568 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7513 (mm) cc_final: 0.7280 (mt)
REVERT: A   35 GLN cc_start: 0.7051 (mt0) cc_final: 0.6514 (mp10)
REVERT: A   40 THR cc_start: 0.8650 (t) cc_final: 0.8305 (m)
REVERT: A  220 HIS cc_start: 0.8928 (m-70) cc_final: 0.8512 (m-70)
REVERT: A  284 ASP cc_start: 0.8698 (m-30) cc_final: 0.8162 (m-30)
REVERT: A  356 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.6881 (ttt180)
REVERT: A  392 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8003 (mt-10)
REVERT: B   49 ARG cc_start: 0.8459 (mpt180) cc_final: 0.8255 (mmt-90)
REVERT: B  155 ASN cc_start: 0.7831 (t0) cc_final: 0.7506 (t0)
REVERT: B  254 ASP cc_start: 0.8670 (t0) cc_final: 0.8242 (t0)
REVERT: B  268 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7808 (m110)
REVERT: B  323 ASP cc_start: 0.7791 (m-30) cc_final: 0.7387 (m-30)
REVERT: B  331 SER cc_start: 0.9220 (t) cc_final: 0.9004 (p)
REVERT: N   50 ASP cc_start: 0.8457 (p0) cc_final: 0.8180 (p0)
REVERT: R  116 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.8084 (mtt-85)
REVERT: R  251 TYR cc_start: 0.8433 (t80) cc_final: 0.8106 (t80)
REVERT: R  254 ARG cc_start: 0.7609 (ptm-80) cc_final: 0.6848 (ptt180)
REVERT: R  268 LEU cc_start: 0.8029 (tt) cc_final: 0.7678 (tp)
  outliers start: 24
  outliers final: 6
  residues processed: 156
  average time/residue: 0.5373
  time to fit residues: 88.8936
Evaluate side-chains
  129 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue  123 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0060
   overall best weight:    1.1800

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 237 ASN
** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.154481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115565 restraints weight = 20476.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 4.64
r_work: 0.3005 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8292  Z= 0.146
  Angle     :  0.633   9.739  11279  Z= 0.304
  Chirality :  0.043   0.276   1282
  Planarity :  0.004   0.042   1433
  Dihedral  :  5.523  54.853   1378
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.38 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1020
  helix:  1.35 (0.26), residues: 406
  sheet: -1.15 (0.33), residues: 233
  loop : -1.16 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 317 
 TYR   0.017   0.001   TYR R 251 
 PHE   0.014   0.002   PHE N 108 
 TRP   0.027   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8289)
  covalent geometry    : angle       0.63332 (11273)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       0.84968 (    6)
  hydrogen bonds       : bond        0.04324 (  386)
  hydrogen bonds       : angle       4.39260 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7465 (mm) cc_final: 0.7217 (mt)
REVERT: A   35 GLN cc_start: 0.7101 (mt0) cc_final: 0.6497 (mp10)
REVERT: A   40 THR cc_start: 0.8608 (t) cc_final: 0.8280 (m)
REVERT: A  209 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7286 (tm-30)
REVERT: A  220 HIS cc_start: 0.8870 (m-70) cc_final: 0.8289 (m-70)
REVERT: A  284 ASP cc_start: 0.8693 (m-30) cc_final: 0.7844 (m-30)
REVERT: A  356 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.6662 (ttt180)
REVERT: A  392 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8005 (mt-10)
REVERT: B  155 ASN cc_start: 0.7858 (t0) cc_final: 0.7527 (t0)
REVERT: B  186 ASP cc_start: 0.8249 (p0) cc_final: 0.7855 (p0)
REVERT: B  254 ASP cc_start: 0.8596 (t0) cc_final: 0.8190 (t0)
REVERT: B  323 ASP cc_start: 0.7583 (m-30) cc_final: 0.7192 (m-30)
REVERT: N    7 SER cc_start: 0.7832 (p) cc_final: 0.7514 (m)
REVERT: R  116 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7987 (mtt-85)
REVERT: R  158 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8309 (mp10)
REVERT: R  254 ARG cc_start: 0.7407 (ptm-80) cc_final: 0.6754 (ptt180)
REVERT: R  268 LEU cc_start: 0.8006 (tt) cc_final: 0.7671 (tp)
  outliers start: 23
  outliers final: 9
  residues processed: 135
  average time/residue: 0.5541
  time to fit residues: 79.3215
Evaluate side-chains
  128 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain R residue  123 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 237 ASN
R  93 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.153827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.106271 restraints weight = 26986.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 3.96
r_work: 0.3012 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8292  Z= 0.135
  Angle     :  0.616   9.996  11279  Z= 0.291
  Chirality :  0.043   0.293   1282
  Planarity :  0.004   0.048   1433
  Dihedral  :  5.442  59.185   1378
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.27 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.26), residues: 1020
  helix:  1.68 (0.26), residues: 406
  sheet: -0.87 (0.33), residues: 231
  loop : -1.03 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 317 
 TYR   0.018   0.001   TYR R 251 
 PHE   0.014   0.001   PHE N 108 
 TRP   0.034   0.002   TRP R 149 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8289)
  covalent geometry    : angle       0.61625 (11273)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       0.94605 (    6)
  hydrogen bonds       : bond        0.03978 (  386)
  hydrogen bonds       : angle       4.22702 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7446 (mm) cc_final: 0.7203 (mt)
REVERT: A   35 GLN cc_start: 0.7138 (mt0) cc_final: 0.6515 (mp10)
REVERT: A   40 THR cc_start: 0.8588 (t) cc_final: 0.8281 (m)
REVERT: A  284 ASP cc_start: 0.8696 (m-30) cc_final: 0.7990 (m-30)
REVERT: A  356 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6674 (ttt180)
REVERT: A  392 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7915 (mt-10)
REVERT: B  155 ASN cc_start: 0.7850 (t0) cc_final: 0.7515 (t0)
REVERT: B  186 ASP cc_start: 0.8208 (p0) cc_final: 0.7804 (p0)
REVERT: B  254 ASP cc_start: 0.8578 (t0) cc_final: 0.8150 (t0)
REVERT: B  323 ASP cc_start: 0.7544 (m-30) cc_final: 0.7187 (m-30)
REVERT: N    7 SER cc_start: 0.7849 (p) cc_final: 0.7537 (m)
REVERT: R   33 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6959 (mp)
REVERT: R  116 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7829 (mtt-85)
REVERT: R  158 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8456 (mp10)
REVERT: R  254 ARG cc_start: 0.7321 (ptm-80) cc_final: 0.6779 (ptt180)
REVERT: R  268 LEU cc_start: 0.8009 (tt) cc_final: 0.7652 (tp)
  outliers start: 31
  outliers final: 8
  residues processed: 140
  average time/residue: 0.4945
  time to fit residues: 73.7861
Evaluate side-chains
  127 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.114931 restraints weight = 20882.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 4.76
r_work: 0.2987 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8292  Z= 0.136
  Angle     :  0.612   9.848  11279  Z= 0.290
  Chirality :  0.043   0.299   1282
  Planarity :  0.004   0.038   1433
  Dihedral  :  5.410  59.972   1378
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.57 %
    Favored  : 80.47 %
  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 are not related in a simple way.
  whole:  0.28 (0.27), residues: 1020
  helix:  1.82 (0.26), residues: 411
  sheet: -0.76 (0.33), residues: 231
  loop : -0.95 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  96 
 TYR   0.017   0.001   TYR R 251 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.041   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8289)
  covalent geometry    : angle       0.61125 (11273)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       1.05841 (    6)
  hydrogen bonds       : bond        0.03941 (  386)
  hydrogen bonds       : angle       4.13684 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7409 (mm) cc_final: 0.7168 (mt)
REVERT: A   35 GLN cc_start: 0.7250 (mt0) cc_final: 0.6628 (mp10)
REVERT: A  209 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7502 (tm-30)
REVERT: A  220 HIS cc_start: 0.8791 (m-70) cc_final: 0.8371 (m-70)
REVERT: A  284 ASP cc_start: 0.8730 (m-30) cc_final: 0.8161 (m-30)
REVERT: A  356 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6856 (ttt180)
REVERT: B  155 ASN cc_start: 0.7889 (t0) cc_final: 0.7581 (t0)
REVERT: B  246 ASP cc_start: 0.8040 (m-30) cc_final: 0.7657 (m-30)
REVERT: B  254 ASP cc_start: 0.8547 (t0) cc_final: 0.8132 (t0)
REVERT: B  323 ASP cc_start: 0.7497 (m-30) cc_final: 0.7047 (m-30)
REVERT: N    7 SER cc_start: 0.7831 (p) cc_final: 0.7510 (m)
REVERT: R   33 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6930 (mp)
REVERT: R  254 ARG cc_start: 0.7329 (ptm-80) cc_final: 0.6756 (ptt180)
REVERT: R  268 LEU cc_start: 0.7989 (tt) cc_final: 0.7630 (tp)
  outliers start: 25
  outliers final: 9
  residues processed: 132
  average time/residue: 0.5329
  time to fit residues: 74.9407
Evaluate side-chains
  126 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:   30.0000
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 340 ASN
** R  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.150435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.103231 restraints weight = 25338.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.83
r_work: 0.2966 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8292  Z= 0.198
  Angle     :  0.669   9.914  11279  Z= 0.323
  Chirality :  0.045   0.308   1282
  Planarity :  0.004   0.060   1433
  Dihedral  :  5.547  58.603   1378
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.40 %
    Favored  : 79.41 %
  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 are not related in a simple way.
  whole:  0.28 (0.26), residues: 1020
  helix:  1.77 (0.26), residues: 411
  sheet: -0.73 (0.33), residues: 231
  loop : -0.93 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 317 
 TYR   0.016   0.002   TYR R 251 
 PHE   0.021   0.002   PHE N 108 
 TRP   0.048   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8289)
  covalent geometry    : angle       0.66895 (11273)
  SS BOND              : bond        0.00365 (    3)
  SS BOND              : angle       0.93032 (    6)
  hydrogen bonds       : bond        0.04488 (  386)
  hydrogen bonds       : angle       4.25986 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7460 (mm) cc_final: 0.7194 (mt)
REVERT: A   35 GLN cc_start: 0.7364 (mt0) cc_final: 0.6705 (mp10)
REVERT: A  209 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7377 (tm-30)
REVERT: A  220 HIS cc_start: 0.8775 (m-70) cc_final: 0.8285 (m-70)
REVERT: A  284 ASP cc_start: 0.8762 (m-30) cc_final: 0.7841 (m-30)
REVERT: A  356 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6562 (ttt180)
REVERT: A  392 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8079 (mt-10)
REVERT: B   67 SER cc_start: 0.8374 (t) cc_final: 0.7766 (m)
REVERT: B  155 ASN cc_start: 0.7994 (t0) cc_final: 0.7656 (t0)
REVERT: B  246 ASP cc_start: 0.8054 (m-30) cc_final: 0.7668 (m-30)
REVERT: B  254 ASP cc_start: 0.8535 (t0) cc_final: 0.8102 (t0)
REVERT: B  323 ASP cc_start: 0.7529 (m-30) cc_final: 0.7278 (m-30)
REVERT: G   21 MET cc_start: 0.7646 (tmt) cc_final: 0.7384 (tmm)
REVERT: N    7 SER cc_start: 0.7820 (p) cc_final: 0.7512 (m)
REVERT: N   69 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8307 (m)
REVERT: N  110 VAL cc_start: 0.9043 (t) cc_final: 0.8450 (m)
REVERT: R   33 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6977 (mp)
REVERT: R  254 ARG cc_start: 0.7382 (ptm-80) cc_final: 0.6795 (ptt180)
REVERT: R  268 LEU cc_start: 0.8030 (tt) cc_final: 0.7642 (tp)
  outliers start: 27
  outliers final: 7
  residues processed: 130
  average time/residue: 0.5475
  time to fit residues: 75.6385
Evaluate side-chains
  125 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue  123 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 16 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 292 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.105673 restraints weight = 29907.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 4.16
r_work: 0.3011 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8292  Z= 0.116
  Angle     :  0.596   9.711  11279  Z= 0.287
  Chirality :  0.042   0.307   1282
  Planarity :  0.004   0.037   1433
  Dihedral  :  5.283  59.978   1378
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.82 %
    Favored  : 79.53 %
  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 are not related in a simple way.
  whole:  0.53 (0.27), residues: 1020
  helix:  2.12 (0.26), residues: 404
  sheet: -0.67 (0.33), residues: 231
  loop : -0.86 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 317 
 TYR   0.014   0.001   TYR R 251 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.048   0.002   TRP R 149 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8289)
  covalent geometry    : angle       0.59602 (11273)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       0.71752 (    6)
  hydrogen bonds       : bond        0.03649 (  386)
  hydrogen bonds       : angle       4.08303 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7545 (mm) cc_final: 0.7323 (mt)
REVERT: A   35 GLN cc_start: 0.7345 (mt0) cc_final: 0.6745 (mp10)
REVERT: A   46 LEU cc_start: 0.8217 (tt) cc_final: 0.7983 (tp)
REVERT: A  209 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7429 (tm-30)
REVERT: A  220 HIS cc_start: 0.8810 (m-70) cc_final: 0.8391 (m-70)
REVERT: A  392 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8052 (mt-10)
REVERT: B   13 GLN cc_start: 0.8110 (tp40) cc_final: 0.7680 (tp40)
REVERT: B   67 SER cc_start: 0.8311 (t) cc_final: 0.7701 (m)
REVERT: B  155 ASN cc_start: 0.8033 (t0) cc_final: 0.7668 (t0)
REVERT: B  246 ASP cc_start: 0.8096 (m-30) cc_final: 0.7715 (m-30)
REVERT: B  254 ASP cc_start: 0.8542 (t0) cc_final: 0.8164 (t0)
REVERT: B  258 ASP cc_start: 0.6675 (t70) cc_final: 0.6468 (t0)
REVERT: B  323 ASP cc_start: 0.7528 (m-30) cc_final: 0.7265 (m-30)
REVERT: G   21 MET cc_start: 0.7724 (tmt) cc_final: 0.7417 (tmm)
REVERT: N    7 SER cc_start: 0.7858 (p) cc_final: 0.7573 (m)
REVERT: R  254 ARG cc_start: 0.7412 (ptm-80) cc_final: 0.6855 (ptt180)
REVERT: R  268 LEU cc_start: 0.8076 (tt) cc_final: 0.7721 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 136
  average time/residue: 0.5184
  time to fit residues: 75.0623
Evaluate side-chains
  123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** R  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.150090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110950 restraints weight = 18637.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 4.15
r_work: 0.2957 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8292  Z= 0.214
  Angle     :  0.675  10.048  11279  Z= 0.329
  Chirality :  0.046   0.309   1282
  Planarity :  0.004   0.035   1433
  Dihedral  :  5.472  55.954   1378
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.05 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 are not related in a simple way.
  whole:  0.36 (0.27), residues: 1020
  helix:  1.93 (0.26), residues: 405
  sheet: -0.76 (0.33), residues: 231
  loop : -0.91 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 317 
 TYR   0.019   0.001   TYR A 339 
 PHE   0.020   0.002   PHE N 108 
 TRP   0.048   0.002   TRP R 149 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 8289)
  covalent geometry    : angle       0.67540 (11273)
  SS BOND              : bond        0.00367 (    3)
  SS BOND              : angle       0.78955 (    6)
  hydrogen bonds       : bond        0.04536 (  386)
  hydrogen bonds       : angle       4.26861 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7546 (mm) cc_final: 0.7269 (mt)
REVERT: A   35 GLN cc_start: 0.7465 (mt0) cc_final: 0.6790 (mp10)
REVERT: A  209 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7710 (tm-30)
REVERT: A  392 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8127 (mt-10)
REVERT: B   13 GLN cc_start: 0.8147 (tp40) cc_final: 0.7689 (tp40)
REVERT: B   67 SER cc_start: 0.8407 (t) cc_final: 0.7984 (m)
REVERT: B  150 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.6747 (mmt90)
REVERT: B  155 ASN cc_start: 0.8041 (t0) cc_final: 0.7679 (t0)
REVERT: B  246 ASP cc_start: 0.8097 (m-30) cc_final: 0.7709 (m-30)
REVERT: B  254 ASP cc_start: 0.8587 (t0) cc_final: 0.8146 (t0)
REVERT: B  268 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (m110)
REVERT: B  323 ASP cc_start: 0.7532 (m-30) cc_final: 0.7316 (m-30)
REVERT: G   21 MET cc_start: 0.7748 (tmt) cc_final: 0.7487 (tmm)
REVERT: N    7 SER cc_start: 0.7861 (p) cc_final: 0.7544 (m)
REVERT: R   33 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6982 (mp)
REVERT: R  254 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.6771 (ptt180)
REVERT: R  268 LEU cc_start: 0.8091 (tt) cc_final: 0.7703 (tp)
  outliers start: 20
  outliers final: 6
  residues processed: 126
  average time/residue: 0.5118
  time to fit residues: 68.6119
Evaluate side-chains
  125 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   33 LEU
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0870
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.155621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.106917 restraints weight = 29879.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 4.54
r_work: 0.2991 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   8292  Z= 0.109
  Angle     :  0.600   9.913  11279  Z= 0.287
  Chirality :  0.042   0.318   1282
  Planarity :  0.004   0.037   1433
  Dihedral  :  5.151  56.859   1378
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 20.83 %
    Favored  : 78.22 %
  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 are not related in a simple way.
  whole:  0.64 (0.27), residues: 1020
  helix:  2.24 (0.26), residues: 404
  sheet: -0.64 (0.34), residues: 226
  loop : -0.82 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 317 
 TYR   0.014   0.001   TYR R 251 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.045   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8289)
  covalent geometry    : angle       0.59984 (11273)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       0.65572 (    6)
  hydrogen bonds       : bond        0.03396 (  386)
  hydrogen bonds       : angle       4.01436 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7319 (mm) cc_final: 0.7118 (mt)
REVERT: A   35 GLN cc_start: 0.7106 (mt0) cc_final: 0.6514 (mp10)
REVERT: A   46 LEU cc_start: 0.8124 (tt) cc_final: 0.7918 (tp)
REVERT: A  209 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7503 (tm-30)
REVERT: A  220 HIS cc_start: 0.8806 (m-70) cc_final: 0.8446 (m-70)
REVERT: A  309 GLU cc_start: 0.7352 (mp0) cc_final: 0.6789 (pm20)
REVERT: A  392 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8028 (mt-10)
REVERT: B   13 GLN cc_start: 0.8021 (tp40) cc_final: 0.7642 (tp40)
REVERT: B   67 SER cc_start: 0.8380 (t) cc_final: 0.7894 (m)
REVERT: B  155 ASN cc_start: 0.7837 (t0) cc_final: 0.7459 (t0)
REVERT: B  246 ASP cc_start: 0.8097 (m-30) cc_final: 0.7669 (m-30)
REVERT: B  254 ASP cc_start: 0.8457 (t0) cc_final: 0.8091 (t0)
REVERT: B  256 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7848 (mtm-85)
REVERT: B  262 MET cc_start: 0.8434 (ttp) cc_final: 0.8195 (ttp)
REVERT: N    7 SER cc_start: 0.7750 (p) cc_final: 0.7458 (m)
REVERT: R  254 ARG cc_start: 0.7326 (ptm-80) cc_final: 0.6601 (ptt180)
REVERT: R  268 LEU cc_start: 0.8005 (tt) cc_final: 0.7678 (tp)
  outliers start: 8
  outliers final: 4
  residues processed: 129
  average time/residue: 0.4860
  time to fit residues: 66.9296
Evaluate side-chains
  123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.155409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.111359 restraints weight = 12835.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.82
r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8292  Z= 0.122
  Angle     :  0.621  10.497  11279  Z= 0.295
  Chirality :  0.042   0.321   1282
  Planarity :  0.004   0.037   1433
  Dihedral  :  5.104  54.452   1378
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 21.18 %
    Favored  : 77.99 %
  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 are not related in a simple way.
  whole:  0.71 (0.27), residues: 1020
  helix:  2.31 (0.26), residues: 404
  sheet: -0.59 (0.34), residues: 224
  loop : -0.82 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 317 
 TYR   0.013   0.001   TYR R 251 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.041   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8289)
  covalent geometry    : angle       0.62067 (11273)
  SS BOND              : bond        0.00193 (    3)
  SS BOND              : angle       0.65800 (    6)
  hydrogen bonds       : bond        0.03544 (  386)
  hydrogen bonds       : angle       4.00716 ( 1111)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7500 (mm) cc_final: 0.7282 (mt)
REVERT: A   35 GLN cc_start: 0.7255 (mt0) cc_final: 0.6623 (mp10)
REVERT: A   46 LEU cc_start: 0.8185 (tt) cc_final: 0.7934 (tp)
REVERT: A  209 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7424 (tm-30)
REVERT: A  220 HIS cc_start: 0.8702 (m-70) cc_final: 0.8313 (m-70)
REVERT: A  309 GLU cc_start: 0.7507 (mp0) cc_final: 0.6908 (pm20)
REVERT: A  392 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (mt-10)
REVERT: B   13 GLN cc_start: 0.8085 (tp40) cc_final: 0.7684 (tp40)
REVERT: B   67 SER cc_start: 0.8218 (t) cc_final: 0.7980 (m)
REVERT: B  155 ASN cc_start: 0.7937 (t0) cc_final: 0.7579 (t0)
REVERT: B  246 ASP cc_start: 0.7975 (m-30) cc_final: 0.7584 (m-30)
REVERT: B  254 ASP cc_start: 0.8367 (t0) cc_final: 0.8032 (t0)
REVERT: B  262 MET cc_start: 0.8309 (ttp) cc_final: 0.8095 (ttp)
REVERT: G   21 MET cc_start: 0.7712 (tmt) cc_final: 0.7362 (tmm)
REVERT: N    7 SER cc_start: 0.7846 (p) cc_final: 0.7563 (m)
REVERT: R  254 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.6800 (ptt180)
REVERT: R  268 LEU cc_start: 0.8014 (tt) cc_final: 0.7699 (tp)
  outliers start: 7
  outliers final: 4
  residues processed: 119
  average time/residue: 0.5137
  time to fit residues: 65.3326
Evaluate side-chains
  118 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    0.0070
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.154812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.116587 restraints weight = 18474.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 4.21
r_work: 0.3044 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8292  Z= 0.111
  Angle     :  0.603   9.603  11279  Z= 0.287
  Chirality :  0.042   0.321   1282
  Planarity :  0.003   0.037   1433
  Dihedral  :  5.001  52.091   1378
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 20.95 %
    Favored  : 78.11 %
  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 are not related in a simple way.
  whole:  0.80 (0.27), residues: 1020
  helix:  2.38 (0.26), residues: 404
  sheet: -0.58 (0.33), residues: 229
  loop : -0.72 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 317 
 TYR   0.013   0.001   TYR R 251 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.048   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8289)
  covalent geometry    : angle       0.60257 (11273)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.64109 (    6)
  hydrogen bonds       : bond        0.03358 (  386)
  hydrogen bonds       : angle       3.94569 ( 1111)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2972.87 seconds
wall clock time: 51 minutes 10.58 seconds (3070.58 seconds total)