Starting phenix.real_space_refine
on Wed Mar 12 21:39:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cfn_30345/03_2025/7cfn_30345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cfn_30345/03_2025/7cfn_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2025/7cfn_30345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2025/7cfn_30345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2025/7cfn_30345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cfn_30345/03_2025/7cfn_30345.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 2, 'ARG: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: 6.79, per 1000 atoms: 0.84
  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: 1.98
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.83
  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: 2.07

  Time building geometry restraints manager: 2.34 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:             0.470
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.420
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:11.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.000
-------------------------------------------------------------------------------
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   8289  Z= 0.486
  Angle     :  1.039   9.772  11273  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 : 7.47
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.040   0.004   TRP A 281 
 HIS   0.013   0.003   HIS A  41 
 PHE   0.026   0.003   PHE B 151 
 TYR   0.021   0.003   TYR A 339 
 ARG   0.013   0.001   ARG A 342 

*********************** 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  : 0.820 
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: 0.3659 (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: 0.6945 (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: 1.2331
  time to fit residues: 225.9482
Evaluate side-chains
  110 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 259 GLN
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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.154583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117515 restraints weight = 23555.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 5.24
r_work: 0.2992 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2991
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2991
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8289  Z= 0.217
  Angle     :  0.657  11.980  11273  Z= 0.318
  Chirality :  0.044   0.283   1282
  Planarity :  0.005   0.049   1433
  Dihedral  :  6.089  51.201   1378
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 11.95 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1020
  helix:  0.68 (0.25), residues: 404
  sheet: -1.29 (0.33), residues: 227
  loop : -1.47 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.020   0.001   TYR R 251 
 ARG   0.006   0.001   ARG A  38 

*********************** 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
  156 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7465 (mm) cc_final: 0.7205 (mt)
REVERT: A   35 GLN cc_start: 0.7147 (mt0) cc_final: 0.6580 (mp10)
REVERT: A   40 THR cc_start: 0.8686 (t) cc_final: 0.8357 (m)
REVERT: A  284 ASP cc_start: 0.8727 (m-30) cc_final: 0.8154 (m-30)
REVERT: A  356 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7080 (ttt180)
REVERT: A  392 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7998 (mt-10)
REVERT: B  155 ASN cc_start: 0.7895 (t0) cc_final: 0.7575 (t0)
REVERT: B  254 ASP cc_start: 0.8670 (t0) cc_final: 0.8262 (t0)
REVERT: B  268 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7846 (m110)
REVERT: B  323 ASP cc_start: 0.7727 (m-30) cc_final: 0.7337 (m-30)
REVERT: G   21 MET cc_start: 0.7198 (ttt) cc_final: 0.6963 (ttm)
REVERT: N   50 ASP cc_start: 0.8513 (p0) cc_final: 0.8303 (p0)
REVERT: R   33 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7146 (mp)
REVERT: R  251 TYR cc_start: 0.8477 (t80) cc_final: 0.8173 (t80)
REVERT: R  254 ARG cc_start: 0.7634 (ptm-80) cc_final: 0.6850 (ptt180)
REVERT: R  268 LEU cc_start: 0.8084 (tt) cc_final: 0.7718 (tp)
  outliers start: 27
  outliers final: 7
  residues processed: 143
  average time/residue: 1.1597
  time to fit residues: 176.7361
Evaluate side-chains
  119 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 62 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.155649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118216 restraints weight = 23498.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 5.25
r_work: 0.3004 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    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 = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8289  Z= 0.179
  Angle     :  0.601   9.989  11273  Z= 0.289
  Chirality :  0.042   0.277   1282
  Planarity :  0.004   0.043   1433
  Dihedral  :  5.498  56.582   1378
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.50 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1020
  helix:  1.53 (0.26), residues: 399
  sheet: -1.08 (0.33), residues: 231
  loop : -1.14 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 246 
 TYR   0.017   0.001   TYR R 251 
 ARG   0.006   0.001   ARG A 317 

*********************** 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
  142 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7454 (mm) cc_final: 0.7217 (mt)
REVERT: A   35 GLN cc_start: 0.7131 (mt0) cc_final: 0.6540 (mp10)
REVERT: A   40 THR cc_start: 0.8573 (t) cc_final: 0.8255 (m)
REVERT: A  209 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7474 (tm-30)
REVERT: A  309 GLU cc_start: 0.7711 (mp0) cc_final: 0.7484 (mp0)
REVERT: A  392 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7944 (mt-10)
REVERT: B   19 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6574 (tpp80)
REVERT: B  155 ASN cc_start: 0.7842 (t0) cc_final: 0.7514 (t0)
REVERT: B  186 ASP cc_start: 0.8223 (p0) cc_final: 0.7763 (p0)
REVERT: B  254 ASP cc_start: 0.8603 (t0) cc_final: 0.8172 (t0)
REVERT: B  262 MET cc_start: 0.8527 (ttm) cc_final: 0.8229 (mtm)
REVERT: B  323 ASP cc_start: 0.7551 (m-30) cc_final: 0.7172 (m-30)
REVERT: N    7 SER cc_start: 0.7829 (p) cc_final: 0.7512 (m)
REVERT: R  254 ARG cc_start: 0.7416 (ptm-80) cc_final: 0.6755 (ptt180)
REVERT: R  268 LEU cc_start: 0.8003 (tt) cc_final: 0.7677 (tp)
  outliers start: 21
  outliers final: 6
  residues processed: 133
  average time/residue: 0.9817
  time to fit residues: 140.6990
Evaluate side-chains
  122 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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   19 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  138 GLU
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 36 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0270
   chunk 53 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7640

-------------------------------------------------------------------------------
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
** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.155809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118056 restraints weight = 18767.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 4.09
r_work: 0.3045 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8289  Z= 0.173
  Angle     :  0.596   9.644  11273  Z= 0.280
  Chirality :  0.042   0.286   1282
  Planarity :  0.004   0.044   1433
  Dihedral  :  5.368  59.851   1378
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.74 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.27), residues: 1020
  helix:  1.81 (0.26), residues: 406
  sheet: -0.76 (0.33), residues: 234
  loop : -0.99 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP R 149 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.017   0.001   TYR R 251 
 ARG   0.010   0.000   ARG A 317 

*********************** 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
  143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7503 (mm) cc_final: 0.7274 (mt)
REVERT: A   35 GLN cc_start: 0.7112 (mt0) cc_final: 0.6516 (mp10)
REVERT: A   40 THR cc_start: 0.8565 (t) cc_final: 0.8240 (m)
REVERT: A  209 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7461 (tm-30)
REVERT: A  309 GLU cc_start: 0.7622 (mp0) cc_final: 0.7358 (mp0)
REVERT: A  392 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7973 (mt-10)
REVERT: B   19 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6689 (tpp80)
REVERT: B  155 ASN cc_start: 0.7845 (t0) cc_final: 0.7542 (t0)
REVERT: B  186 ASP cc_start: 0.8240 (p0) cc_final: 0.7841 (p0)
REVERT: B  254 ASP cc_start: 0.8549 (t0) cc_final: 0.8151 (t0)
REVERT: B  262 MET cc_start: 0.8474 (ttm) cc_final: 0.8149 (ttp)
REVERT: B  323 ASP cc_start: 0.7578 (m-30) cc_final: 0.7228 (m-30)
REVERT: N    7 SER cc_start: 0.7841 (p) cc_final: 0.7538 (m)
REVERT: R  158 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8433 (mp10)
REVERT: R  254 ARG cc_start: 0.7333 (ptm-80) cc_final: 0.6821 (ptt180)
REVERT: R  268 LEU cc_start: 0.8022 (tt) cc_final: 0.7714 (tp)
  outliers start: 22
  outliers final: 6
  residues processed: 133
  average time/residue: 1.0979
  time to fit residues: 156.3705
Evaluate side-chains
  126 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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   19 ARG
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain N residue   69 THR
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 62 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 16 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.152978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115321 restraints weight = 20603.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 4.69
r_work: 0.2983 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    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 = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8289  Z= 0.233
  Angle     :  0.616   9.770  11273  Z= 0.292
  Chirality :  0.043   0.305   1282
  Planarity :  0.004   0.038   1433
  Dihedral  :  5.433  59.213   1378
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.16 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.27), residues: 1020
  helix:  1.87 (0.26), residues: 411
  sheet: -0.67 (0.33), residues: 234
  loop : -0.95 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP R 149 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.014   0.002   PHE N 108 
 TYR   0.016   0.001   TYR R 251 
 ARG   0.007   0.000   ARG A 317 

*********************** 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: 22
    poor density    : 122
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7416 (mm) cc_final: 0.7169 (mt)
REVERT: A   35 GLN cc_start: 0.7250 (mt0) cc_final: 0.6630 (mp10)
REVERT: A   46 LEU cc_start: 0.8271 (tt) cc_final: 0.8013 (tp)
REVERT: A  309 GLU cc_start: 0.7631 (mp0) cc_final: 0.7360 (mp0)
REVERT: B   19 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6653 (tpp80)
REVERT: B   67 SER cc_start: 0.8448 (t) cc_final: 0.8246 (t)
REVERT: B  155 ASN cc_start: 0.7841 (t0) cc_final: 0.7512 (t0)
REVERT: B  186 ASP cc_start: 0.8258 (p0) cc_final: 0.7822 (p0)
REVERT: B  246 ASP cc_start: 0.8013 (m-30) cc_final: 0.7648 (m-30)
REVERT: B  254 ASP cc_start: 0.8550 (t0) cc_final: 0.8114 (t0)
REVERT: B  262 MET cc_start: 0.8454 (ttm) cc_final: 0.8074 (ttp)
REVERT: B  323 ASP cc_start: 0.7529 (m-30) cc_final: 0.7115 (m-30)
REVERT: G   21 MET cc_start: 0.7715 (tmt) cc_final: 0.7354 (tmm)
REVERT: N    7 SER cc_start: 0.7839 (p) cc_final: 0.7518 (m)
REVERT: R  158 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8443 (mp10)
REVERT: R  254 ARG cc_start: 0.7339 (ptm-80) cc_final: 0.6767 (ptt180)
REVERT: R  268 LEU cc_start: 0.8002 (tt) cc_final: 0.7652 (tp)
  outliers start: 22
  outliers final: 6
  residues processed: 133
  average time/residue: 1.0522
  time to fit residues: 149.9367
Evaluate side-chains
  124 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 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 N residue   69 THR
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 59 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 86 optimal weight:    7.9990
   chunk 16 optimal weight:   30.0000
   chunk 92 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.155032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.117674 restraints weight = 21924.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 4.92
r_work: 0.2999 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    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 = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8289  Z= 0.169
  Angle     :  0.591   9.584  11273  Z= 0.280
  Chirality :  0.042   0.310   1282
  Planarity :  0.004   0.053   1433
  Dihedral  :  5.289  57.779   1378
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.22 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.27), residues: 1020
  helix:  2.06 (0.26), residues: 411
  sheet: -0.55 (0.34), residues: 229
  loop : -0.90 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP R 149 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.015   0.001   TYR R 251 
 ARG   0.014   0.000   ARG A 317 

*********************** 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
  138 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7431 (mm) cc_final: 0.7205 (mt)
REVERT: A   35 GLN cc_start: 0.7170 (mt0) cc_final: 0.6585 (mp10)
REVERT: A   46 LEU cc_start: 0.8204 (tt) cc_final: 0.7974 (tp)
REVERT: A  309 GLU cc_start: 0.7598 (mp0) cc_final: 0.7333 (mp0)
REVERT: A  392 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8022 (mt-10)
REVERT: B  155 ASN cc_start: 0.7901 (t0) cc_final: 0.7545 (t0)
REVERT: B  186 ASP cc_start: 0.8240 (p0) cc_final: 0.7828 (p0)
REVERT: B  246 ASP cc_start: 0.8051 (m-30) cc_final: 0.7681 (m-30)
REVERT: B  254 ASP cc_start: 0.8534 (t0) cc_final: 0.8122 (t0)
REVERT: B  262 MET cc_start: 0.8412 (ttm) cc_final: 0.8021 (ttp)
REVERT: B  323 ASP cc_start: 0.7490 (m-30) cc_final: 0.7115 (m-30)
REVERT: N    7 SER cc_start: 0.7816 (p) cc_final: 0.7501 (m)
REVERT: R  254 ARG cc_start: 0.7308 (ptm-80) cc_final: 0.6737 (ptt180)
REVERT: R  268 LEU cc_start: 0.7961 (tt) cc_final: 0.7654 (tp)
  outliers start: 15
  outliers final: 4
  residues processed: 131
  average time/residue: 1.0339
  time to fit residues: 145.1856
Evaluate side-chains
  122 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  157 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.154314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.117421 restraints weight = 23952.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 5.18
r_work: 0.2979 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8289  Z= 0.189
  Angle     :  0.594   9.702  11273  Z= 0.283
  Chirality :  0.042   0.308   1282
  Planarity :  0.004   0.036   1433
  Dihedral  :  5.275  58.135   1378
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.17 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.27), residues: 1020
  helix:  2.15 (0.26), residues: 411
  sheet: -0.49 (0.34), residues: 229
  loop : -0.89 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP R 149 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.014   0.001   TYR R 251 
 ARG   0.007   0.000   ARG B  96 

*********************** 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
  131 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7516 (mm) cc_final: 0.7284 (mt)
REVERT: A   35 GLN cc_start: 0.7279 (mt0) cc_final: 0.6672 (mp10)
REVERT: A   46 LEU cc_start: 0.8271 (tt) cc_final: 0.8055 (tp)
REVERT: A  209 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7619 (tm-30)
REVERT: A  309 GLU cc_start: 0.7616 (mp0) cc_final: 0.7329 (mp0)
REVERT: A  392 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8089 (mt-10)
REVERT: B   67 SER cc_start: 0.8322 (t) cc_final: 0.7871 (m)
REVERT: B  155 ASN cc_start: 0.7882 (t0) cc_final: 0.7530 (t0)
REVERT: B  246 ASP cc_start: 0.8110 (m-30) cc_final: 0.7723 (m-30)
REVERT: B  254 ASP cc_start: 0.8590 (t0) cc_final: 0.8187 (t0)
REVERT: B  258 ASP cc_start: 0.6610 (t70) cc_final: 0.6404 (t0)
REVERT: B  262 MET cc_start: 0.8394 (ttm) cc_final: 0.8025 (ttp)
REVERT: G   21 MET cc_start: 0.7713 (tmt) cc_final: 0.7322 (tmm)
REVERT: N    7 SER cc_start: 0.7813 (p) cc_final: 0.7535 (m)
REVERT: R  254 ARG cc_start: 0.7340 (ptm-80) cc_final: 0.6766 (ptt180)
REVERT: R  268 LEU cc_start: 0.7974 (tt) cc_final: 0.7668 (tp)
  outliers start: 10
  outliers final: 5
  residues processed: 128
  average time/residue: 1.0588
  time to fit residues: 145.1386
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  : 0.873 
-------------------------------------------------------------------------------
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   19 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  123 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.155607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.109478 restraints weight = 25010.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 3.74
r_work: 0.3052 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   8289  Z= 0.157
  Angle     :  0.581   9.840  11273  Z= 0.277
  Chirality :  0.041   0.313   1282
  Planarity :  0.003   0.036   1433
  Dihedral  :  5.154  58.079   1378
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.05 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 1020
  helix:  2.35 (0.26), residues: 404
  sheet: -0.38 (0.34), residues: 227
  loop : -0.83 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP R 149 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.014   0.001   TYR R 251 
 ARG   0.008   0.000   ARG B  96 

*********************** 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
  136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7479 (mm) cc_final: 0.7262 (mt)
REVERT: A   35 GLN cc_start: 0.7206 (mt0) cc_final: 0.6589 (mp10)
REVERT: A   46 LEU cc_start: 0.8225 (tt) cc_final: 0.7990 (tp)
REVERT: A  209 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7512 (tm-30)
REVERT: A  309 GLU cc_start: 0.7610 (mp0) cc_final: 0.7336 (mp0)
REVERT: A  392 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8008 (mt-10)
REVERT: B   13 GLN cc_start: 0.8155 (tp40) cc_final: 0.7688 (tp40)
REVERT: B   67 SER cc_start: 0.8258 (t) cc_final: 0.7987 (m)
REVERT: B  155 ASN cc_start: 0.7929 (t0) cc_final: 0.7588 (t0)
REVERT: B  246 ASP cc_start: 0.8033 (m-30) cc_final: 0.7645 (m-30)
REVERT: B  254 ASP cc_start: 0.8509 (t0) cc_final: 0.8113 (t0)
REVERT: B  262 MET cc_start: 0.8329 (ttm) cc_final: 0.7931 (ttp)
REVERT: G   21 MET cc_start: 0.7684 (tmt) cc_final: 0.7314 (tmm)
REVERT: N    7 SER cc_start: 0.7796 (p) cc_final: 0.7530 (m)
REVERT: R  254 ARG cc_start: 0.7345 (ptm-80) cc_final: 0.6799 (ptt180)
REVERT: R  268 LEU cc_start: 0.7967 (tt) cc_final: 0.7669 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 131
  average time/residue: 1.2672
  time to fit residues: 177.9190
Evaluate side-chains
  124 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 N residue   69 THR
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 45 optimal weight:    6.9990
   chunk 32 optimal weight:    0.1980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
N  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.152824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.114173 restraints weight = 14613.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 3.08
r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8289  Z= 0.217
  Angle     :  0.628  10.308  11273  Z= 0.300
  Chirality :  0.043   0.317   1282
  Planarity :  0.004   0.058   1433
  Dihedral  :  5.239  59.535   1378
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.05 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 1020
  helix:  2.21 (0.26), residues: 410
  sheet: -0.44 (0.34), residues: 229
  loop : -0.82 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP R 149 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.001   PHE N 108 
 TYR   0.014   0.001   TYR R 251 
 ARG   0.015   0.001   ARG A 317 

*********************** 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
  130 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.7461 (mm) cc_final: 0.7222 (mt)
REVERT: A   35 GLN cc_start: 0.7317 (mt0) cc_final: 0.6661 (mp10)
REVERT: A   46 LEU cc_start: 0.8239 (tt) cc_final: 0.8003 (tp)
REVERT: A  309 GLU cc_start: 0.7651 (mp0) cc_final: 0.7364 (mp0)
REVERT: A  392 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7980 (mt-10)
REVERT: B   13 GLN cc_start: 0.8226 (tp40) cc_final: 0.7759 (tp40)
REVERT: B  155 ASN cc_start: 0.7990 (t0) cc_final: 0.7641 (t0)
REVERT: B  246 ASP cc_start: 0.7943 (m-30) cc_final: 0.7554 (m-30)
REVERT: B  254 ASP cc_start: 0.8440 (t0) cc_final: 0.8057 (t0)
REVERT: B  262 MET cc_start: 0.8258 (ttm) cc_final: 0.7855 (ttp)
REVERT: G   21 MET cc_start: 0.7675 (tmt) cc_final: 0.7344 (tmm)
REVERT: N    7 SER cc_start: 0.7828 (p) cc_final: 0.7556 (m)
REVERT: R  254 ARG cc_start: 0.7372 (ptm-80) cc_final: 0.6836 (ptt180)
REVERT: R  268 LEU cc_start: 0.8018 (tt) cc_final: 0.7710 (tp)
  outliers start: 14
  outliers final: 4
  residues processed: 122
  average time/residue: 1.6916
  time to fit residues: 219.7215
Evaluate side-chains
  120 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 3.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
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 R residue  123 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0270
   chunk 49 optimal weight:    0.3980
   chunk 55 optimal weight:    6.9990
   chunk 19 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.156481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.117546 restraints weight = 19134.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 4.21
r_work: 0.3059 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   8289  Z= 0.152
  Angle     :  0.587   9.366  11273  Z= 0.280
  Chirality :  0.042   0.324   1282
  Planarity :  0.004   0.038   1433
  Dihedral  :  5.088  59.033   1378
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 20.12 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1020
  helix:  2.47 (0.26), residues: 403
  sheet: -0.35 (0.34), residues: 227
  loop : -0.80 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP R 149 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.013   0.001   TYR R 251 
 ARG   0.008   0.001   ARG B  96 

********************** 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
  121 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.7274 (mt0) cc_final: 0.6627 (mp10)
REVERT: A   46 LEU cc_start: 0.8221 (tt) cc_final: 0.7993 (tp)
REVERT: A  309 GLU cc_start: 0.7562 (mp0) cc_final: 0.7251 (mp0)
REVERT: B   45 MET cc_start: 0.8319 (ptp) cc_final: 0.7925 (mtt)
REVERT: B  155 ASN cc_start: 0.8020 (t0) cc_final: 0.7655 (t0)
REVERT: B  246 ASP cc_start: 0.8056 (m-30) cc_final: 0.7712 (m-30)
REVERT: B  254 ASP cc_start: 0.8429 (t0) cc_final: 0.8099 (t0)
REVERT: B  256 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7936 (mtm-85)
REVERT: B  262 MET cc_start: 0.8257 (ttm) cc_final: 0.7863 (ttp)
REVERT: N    7 SER cc_start: 0.7855 (p) cc_final: 0.7580 (m)
REVERT: N   31 ASN cc_start: 0.8394 (m-40) cc_final: 0.8099 (m110)
REVERT: R  249 LEU cc_start: 0.7859 (tp) cc_final: 0.7614 (tt)
REVERT: R  254 ARG cc_start: 0.7341 (ptm-80) cc_final: 0.6639 (ptt180)
REVERT: R  268 LEU cc_start: 0.7976 (tt) cc_final: 0.7680 (tp)
  outliers start: 6
  outliers final: 2
  residues processed: 119
  average time/residue: 1.0854
  time to fit residues: 138.0733
Evaluate side-chains
  114 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain R residue  123 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 16 optimal weight:   40.0000
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.156380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.117085 restraints weight = 21655.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 4.72
r_work: 0.3026 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8289  Z= 0.160
  Angle     :  0.583   9.465  11273  Z= 0.280
  Chirality :  0.042   0.321   1282
  Planarity :  0.004   0.036   1433
  Dihedral  :  5.014  56.984   1378
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 19.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.27), residues: 1020
  helix:  2.55 (0.26), residues: 398
  sheet: -0.38 (0.34), residues: 229
  loop : -0.74 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP R 149 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.013   0.001   TYR R 251 
 ARG   0.009   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6347.56 seconds
wall clock time: 112 minutes 54.58 seconds (6774.58 seconds total)