Starting phenix.real_space_refine
on Tue Feb 11 19:32:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uo2_42425/02_2025/8uo2_42425.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uo2_42425/02_2025/8uo2_42425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uo2_42425/02_2025/8uo2_42425.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uo2_42425/02_2025/8uo2_42425.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uo2_42425/02_2025/8uo2_42425.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uo2_42425/02_2025/8uo2_42425.cif"
  }
  resolution = 3.6
  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=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      32      5.16       5
     C    4126      2.51       5
     N    1154      2.21       5
     O    1189      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6504
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 1920
          Classifications: {'peptide': 283}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 117}
          Link IDs: {'PTRANS': 6, 'TRANS': 276}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 435
          Unresolved non-hydrogen angles: 536
          Unresolved non-hydrogen dihedrals: 343
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 18, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 278
    Chain: "B"
      Number of atoms: 2396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2396
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 242
          Unresolved non-hydrogen dihedrals: 150
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 11}
          Unresolved non-hydrogen planarities: 145
    Chain: "G"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 341
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 1800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 1800
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 492
          Unresolved non-hydrogen angles: 629
          Unresolved non-hydrogen dihedrals: 406
          Unresolved non-hydrogen chiralities: 54
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 252
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.04, per 1000 atoms: 0.77
  Number of scatterers: 6504
  At special positions: 0
  Unit cell: (84.1669, 135.361, 98.0501, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       3     15.00
     O    1189      8.00
     N    1154      7.00
     C    4126      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 1.68
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1818

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      49.4% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.698A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 90 through 109
    Processing helix  chain 'A' and resid 161 through 165
      removed outlier: 3.736A  pdb=" N   ARG A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 161 through 165'
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 3.775A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.692A  pdb=" N   SER A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.591A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.257A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.507A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 391
      removed outlier: 3.760A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.661A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    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 10 through 24
      removed outlier: 3.760A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU G  19 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.661A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 4.032A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ALA R  59 " --> pdb=" O   ILE R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.850A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.748A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.281A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.635A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.746A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLU R 237 " --> pdb=" O   ILE R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 4.025A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.858A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN R 299 " --> pdb=" O   VAL R 295 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.605A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 326
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.505A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213
      removed outlier: 6.370A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.875A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.810A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.693A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 6.951A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.865A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.970A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA B 208 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243
      removed outlier: 3.848A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277

    349 hydrogen bonds defined for protein.
    1020 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.84 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: 1697
        1.33 -     1.45: 1252
        1.45 -     1.57: 3635
        1.57 -     1.69: 5
        1.69 -     1.81: 40
  Bond restraints: 6629
  Sorted by residual:
  bond pdb=" C   ALA A 366 "
       pdb=" N   VAL A 367 "
    ideal  model  delta    sigma   weight residual
    1.334  1.450 -0.116 1.26e-02 6.30e+03 8.45e+01
  bond pdb=" CA  LYS A 338 "
       pdb=" C   LYS A 338 "
    ideal  model  delta    sigma   weight residual
    1.524  1.483  0.040 1.27e-02 6.20e+03 1.01e+01
  bond pdb=" N   VAL B 133 "
       pdb=" CA  VAL B 133 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.22e-02 6.72e+03 9.81e+00
  bond pdb=" N   ILE A 257 "
       pdb=" CA  ILE A 257 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.037 1.19e-02 7.06e+03 9.42e+00
  bond pdb=" CA  SER B 245 "
       pdb=" CB  SER B 245 "
    ideal  model  delta    sigma   weight residual
    1.535  1.471  0.064 2.09e-02 2.29e+03 9.32e+00
  ... (remaining 6624 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 8834
        2.13 -     4.26: 222
        4.26 -     6.39: 35
        6.39 -     8.52: 9
        8.52 -    10.65: 3
  Bond angle restraints: 9103
  Sorted by residual:
  angle pdb=" N   ASN A  23 "
        pdb=" CA  ASN A  23 "
        pdb=" C   ASN A  23 "
      ideal   model   delta    sigma   weight residual
     111.28  104.51    6.77 1.09e+00 8.42e-01 3.86e+01
  angle pdb=" N   GLN A 267 "
        pdb=" CA  GLN A 267 "
        pdb=" C   GLN A 267 "
      ideal   model   delta    sigma   weight residual
     111.71  105.87    5.84 1.15e+00 7.56e-01 2.57e+01
  angle pdb=" N   GLU A 268 "
        pdb=" CA  GLU A 268 "
        pdb=" C   GLU A 268 "
      ideal   model   delta    sigma   weight residual
     111.28  106.51    4.77 1.09e+00 8.42e-01 1.92e+01
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     109.23  115.77   -6.54 1.55e+00 4.16e-01 1.78e+01
  angle pdb=" C   SER R 236 "
        pdb=" N   GLU R 237 "
        pdb=" CA  GLU R 237 "
      ideal   model   delta    sigma   weight residual
     123.11  117.24    5.87 1.42e+00 4.96e-01 1.71e+01
  ... (remaining 9098 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.33: 3757
       33.33 -    66.67: 62
       66.67 -   100.00: 4
      100.00 -   133.33: 1
      133.33 -   166.67: 2
  Dihedral angle restraints: 3826
    sinusoidal: 1036
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -97.40  166.67     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -54.17  158.76     1      2.00e+01 2.50e-03 4.64e+01
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  159.15  114.97     1      2.00e+01 2.50e-03 3.41e+01
  ... (remaining 3823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 898
       0.055 -    0.110: 165
       0.110 -    0.165: 39
       0.165 -    0.220: 5
       0.220 -    0.275: 1
  Chirality restraints: 1108
  Sorted by residual:
  chirality pdb=" CA  ILE B 229 "
            pdb=" N   ILE B 229 "
            pdb=" C   ILE B 229 "
            pdb=" CB  ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  ILE A 257 "
            pdb=" N   ILE A 257 "
            pdb=" C   ILE A 257 "
            pdb=" CB  ILE A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  VAL B 133 "
            pdb=" N   VAL B 133 "
            pdb=" C   VAL B 133 "
            pdb=" CB  VAL B 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1105 not shown)

  Planarity restraints: 1167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 366 "    0.014 2.00e-02 2.50e+03   2.74e-02 7.52e+00
        pdb=" C   ALA A 366 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ALA A 366 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 367 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 219 "    0.011 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   ARG B 219 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG B 219 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLN B 220 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 266 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.84e+00
        pdb=" C   LEU A 266 "    0.038 2.00e-02 2.50e+03
        pdb=" O   LEU A 266 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A 267 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1164 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1204
        2.77 -     3.30: 6111
        3.30 -     3.83: 10308
        3.83 -     4.37: 10547
        4.37 -     4.90: 19304
  Nonbonded interactions: 47474
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   LEU A  45 "
            pdb=" CG2 VAL A 224 "
     model   vdw
     2.274 3.460
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" NE2 HIS B 142 "
            pdb=" OG  SER B 161 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" N   SER A  54 "
            pdb=" O1B GTP A 401 "
     model   vdw
     2.377 3.120
  ... (remaining 47469 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.730
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
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      :  0.005   0.116   6629  Z= 0.354
  Angle     :  0.761  10.646   9103  Z= 0.488
  Chirality :  0.047   0.275   1108
  Planarity :  0.003   0.035   1167
  Dihedral  : 13.649 166.667   2005
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.20 %
    Favored  : 98.40 %
  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:  1.29 (0.28), residues: 936
  helix:  2.46 (0.25), residues: 414
  sheet: -0.21 (0.42), residues: 168
  loop : -0.52 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.012   0.001   PHE A 246 
 TYR   0.011   0.001   TYR R 316 
 ARG   0.005   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.675 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.9036 (t70) cc_final: 0.8362 (t0)
REVERT: R  217 PHE cc_start: 0.7921 (t80) cc_final: 0.7677 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1317
  time to fit residues: 18.7266
Evaluate side-chains
  73 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 71 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0870
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:   30.0000
   chunk 44 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.4560

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.116821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.092822 restraints weight = 13845.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095615 restraints weight = 7484.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097564 restraints weight = 5056.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6629  Z= 0.230
  Angle     :  0.495   5.776   9103  Z= 0.276
  Chirality :  0.042   0.185   1108
  Planarity :  0.003   0.037   1167
  Dihedral  :  8.929 158.706   1031
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.02 %
    Favored  : 87.37 %
  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:  1.37 (0.28), residues: 936
  helix:  2.78 (0.25), residues: 418
  sheet: -0.23 (0.41), residues: 169
  loop : -0.86 (0.30), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.013   0.002   PHE B 235 
 TYR   0.023   0.001   TYR R 308 
 ARG   0.003   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.714 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.8920 (t70) cc_final: 0.8324 (t0)
REVERT: R  209 TYR cc_start: 0.7956 (m-80) cc_final: 0.7725 (m-10)
  outliers start: 8
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1385
  time to fit residues: 16.2806
Evaluate side-chains
  76 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:   20.0000
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0370
   chunk 88 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.0662

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.117092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.092792 restraints weight = 14117.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095595 restraints weight = 7618.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.097544 restraints weight = 5135.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6629  Z= 0.170
  Angle     :  0.440   5.894   9103  Z= 0.242
  Chirality :  0.040   0.139   1108
  Planarity :  0.003   0.042   1167
  Dihedral  :  8.475 155.162   1031
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.23 %
    Favored  : 83.57 %
  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:  1.54 (0.28), residues: 936
  helix:  2.95 (0.25), residues: 419
  sheet: -0.29 (0.40), residues: 170
  loop : -0.74 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.012   0.001   PHE A 246 
 TYR   0.022   0.001   TYR R 308 
 ARG   0.010   0.001   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.697 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8858 (tmm) cc_final: 0.8607 (tmm)
REVERT: B  262 MET cc_start: 0.8155 (tpp) cc_final: 0.7942 (tpp)
REVERT: B  298 ASP cc_start: 0.8331 (t0) cc_final: 0.7762 (t0)
REVERT: G   48 ASP cc_start: 0.8965 (t70) cc_final: 0.8247 (t0)
REVERT: R  209 TYR cc_start: 0.8037 (m-80) cc_final: 0.7835 (m-10)
  outliers start: 6
  outliers final: 6
  residues processed: 79
  average time/residue: 0.1486
  time to fit residues: 17.1876
Evaluate side-chains
  77 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.091398 restraints weight = 14201.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.094113 restraints weight = 7669.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.095967 restraints weight = 5208.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6629  Z= 0.182
  Angle     :  0.440   5.970   9103  Z= 0.242
  Chirality :  0.040   0.134   1108
  Planarity :  0.003   0.042   1167
  Dihedral  :  8.208 153.518   1031
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.43 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.58 (0.28), residues: 936
  helix:  3.07 (0.25), residues: 419
  sheet: -0.37 (0.40), residues: 172
  loop : -0.81 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 313 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.023   0.001   TYR R 308 
 ARG   0.008   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.790 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8931 (tmm) cc_final: 0.8688 (tmm)
REVERT: B  262 MET cc_start: 0.8237 (tpp) cc_final: 0.7941 (tpp)
REVERT: B  298 ASP cc_start: 0.8367 (t0) cc_final: 0.7796 (t0)
REVERT: G   48 ASP cc_start: 0.8956 (t70) cc_final: 0.8158 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 80
  average time/residue: 0.1505
  time to fit residues: 17.4073
Evaluate side-chains
  77 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 75 optimal weight:    0.3980
   chunk 56 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0370
   chunk 86 optimal weight:    0.0050
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.4272

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.118541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.094235 restraints weight = 14001.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.097013 restraints weight = 7526.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.098980 restraints weight = 5092.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6629  Z= 0.108
  Angle     :  0.406   5.946   9103  Z= 0.221
  Chirality :  0.039   0.133   1108
  Planarity :  0.003   0.037   1167
  Dihedral  :  7.925 150.253   1031
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.03 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.78 (0.28), residues: 936
  helix:  3.22 (0.25), residues: 419
  sheet: -0.09 (0.41), residues: 168
  loop : -0.77 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 313 
 HIS   0.002   0.000   HIS B 225 
 PHE   0.008   0.001   PHE B 199 
 TYR   0.023   0.001   TYR R 308 
 ARG   0.008   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.672 
Fit side-chains
REVERT: B  262 MET cc_start: 0.8191 (tpp) cc_final: 0.7901 (tpp)
REVERT: B  298 ASP cc_start: 0.8345 (t0) cc_final: 0.7628 (t0)
REVERT: G   48 ASP cc_start: 0.8862 (t70) cc_final: 0.8169 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1314
  time to fit residues: 16.8404
Evaluate side-chains
  79 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.115100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.090828 restraints weight = 14104.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.093505 restraints weight = 7674.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.095313 restraints weight = 5237.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6629  Z= 0.210
  Angle     :  0.453   5.999   9103  Z= 0.249
  Chirality :  0.041   0.139   1108
  Planarity :  0.003   0.042   1167
  Dihedral  :  7.862 151.634   1031
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.43 %
    Favored  : 81.16 %
  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:  1.79 (0.28), residues: 936
  helix:  3.29 (0.26), residues: 418
  sheet: -0.24 (0.40), residues: 170
  loop : -0.76 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.022   0.001   TYR R 308 
 ARG   0.006   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.686 
Fit side-chains
REVERT: B  262 MET cc_start: 0.8234 (tpp) cc_final: 0.7886 (tpp)
REVERT: B  298 ASP cc_start: 0.8467 (t0) cc_final: 0.7908 (t0)
REVERT: G   48 ASP cc_start: 0.8923 (t70) cc_final: 0.8108 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1345
  time to fit residues: 15.7515
Evaluate side-chains
  78 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 61 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   chunk 4 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.117693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.093328 restraints weight = 13897.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.096110 restraints weight = 7540.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098065 restraints weight = 5112.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6629  Z= 0.111
  Angle     :  0.412   5.892   9103  Z= 0.223
  Chirality :  0.040   0.130   1108
  Planarity :  0.003   0.038   1167
  Dihedral  :  7.654 148.970   1031
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.64 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.88 (0.28), residues: 936
  helix:  3.35 (0.25), residues: 418
  sheet: -0.06 (0.41), residues: 168
  loop : -0.77 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.002   0.000   HIS B 225 
 PHE   0.020   0.001   PHE R 217 
 TYR   0.024   0.001   TYR R 308 
 ARG   0.010   0.000   ARG R 131 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.761 
Fit side-chains
REVERT: B  262 MET cc_start: 0.8209 (tpp) cc_final: 0.7879 (tpp)
REVERT: B  298 ASP cc_start: 0.8423 (t0) cc_final: 0.7758 (t0)
REVERT: G   48 ASP cc_start: 0.8851 (t70) cc_final: 0.8118 (t0)
  outliers start: 10
  outliers final: 10
  residues processed: 81
  average time/residue: 0.1375
  time to fit residues: 16.3063
Evaluate side-chains
  79 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    0.0000
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0270
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.7444

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.092750 restraints weight = 14063.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.095547 restraints weight = 7644.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.097396 restraints weight = 5174.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6629  Z= 0.133
  Angle     :  0.422   5.931   9103  Z= 0.228
  Chirality :  0.040   0.130   1108
  Planarity :  0.003   0.038   1167
  Dihedral  :  7.516 148.196   1031
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.64 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.91 (0.28), residues: 936
  helix:  3.39 (0.25), residues: 418
  sheet: -0.12 (0.41), residues: 170
  loop : -0.74 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 313 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.019   0.001   PHE R 217 
 TYR   0.023   0.001   TYR R 308 
 ARG   0.009   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.717 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8771 (m100) cc_final: 0.8513 (m100)
REVERT: B  262 MET cc_start: 0.8234 (tpp) cc_final: 0.7887 (tpp)
REVERT: B  298 ASP cc_start: 0.8450 (t0) cc_final: 0.7784 (t0)
REVERT: G   48 ASP cc_start: 0.8866 (t70) cc_final: 0.8114 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1331
  time to fit residues: 15.7480
Evaluate side-chains
  80 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0370
   chunk 91 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0050
   chunk 93 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.4872

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.118486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.094116 restraints weight = 14119.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.096925 restraints weight = 7591.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.098873 restraints weight = 5130.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6629  Z= 0.108
  Angle     :  0.409   5.906   9103  Z= 0.220
  Chirality :  0.039   0.134   1108
  Planarity :  0.003   0.037   1167
  Dihedral  :  7.329 146.054   1031
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.04 %
    Favored  : 80.16 %
  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:  1.97 (0.28), residues: 936
  helix:  3.43 (0.25), residues: 418
  sheet:  0.04 (0.41), residues: 168
  loop : -0.75 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 313 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.020   0.001   PHE R 217 
 TYR   0.024   0.001   TYR R 308 
 ARG   0.008   0.000   ARG R 131 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.699 
Fit side-chains
REVERT: B  169 TRP cc_start: 0.8729 (m100) cc_final: 0.8445 (m100)
REVERT: B  262 MET cc_start: 0.8215 (tpp) cc_final: 0.7886 (tpp)
REVERT: B  298 ASP cc_start: 0.8409 (t0) cc_final: 0.7684 (t0)
REVERT: G   48 ASP cc_start: 0.8836 (t70) cc_final: 0.8076 (t0)
REVERT: R  316 TYR cc_start: 0.8464 (m-10) cc_final: 0.8177 (m-80)
  outliers start: 9
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1323
  time to fit residues: 16.3859
Evaluate side-chains
  82 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.114599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.090292 restraints weight = 14259.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.092986 restraints weight = 7784.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.094833 restraints weight = 5307.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6629  Z= 0.222
  Angle     :  0.465   5.999   9103  Z= 0.255
  Chirality :  0.041   0.134   1108
  Planarity :  0.003   0.041   1167
  Dihedral  :  7.485 149.440   1031
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.24 %
    Favored  : 79.96 %
  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:  1.91 (0.29), residues: 936
  helix:  3.39 (0.26), residues: 418
  sheet: -0.11 (0.41), residues: 170
  loop : -0.74 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.020   0.002   PHE R 217 
 TYR   0.023   0.001   TYR R 308 
 ARG   0.008   0.000   ARG A 342 

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.705 
Fit side-chains
REVERT: B  262 MET cc_start: 0.8241 (tpp) cc_final: 0.7871 (tpp)
REVERT: G   48 ASP cc_start: 0.8889 (t70) cc_final: 0.8026 (t0)
  outliers start: 9
  outliers final: 9
  residues processed: 78
  average time/residue: 0.1269
  time to fit residues: 14.8081
Evaluate side-chains
  80 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0010
   chunk 87 optimal weight:    0.7980
   chunk 93 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.116903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.092511 restraints weight = 14244.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.095332 restraints weight = 7685.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.097269 restraints weight = 5168.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6629  Z= 0.125
  Angle     :  0.421   5.890   9103  Z= 0.228
  Chirality :  0.040   0.134   1108
  Planarity :  0.003   0.039   1167
  Dihedral  :  7.348 147.777   1031
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.84 %
    Favored  : 80.16 %
  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:  1.96 (0.28), residues: 936
  helix:  3.43 (0.25), residues: 418
  sheet:  0.02 (0.41), residues: 168
  loop : -0.78 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 313 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.020   0.001   PHE R 217 
 TYR   0.024   0.001   TYR R 308 
 ARG   0.007   0.000   ARG R 131 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2322.93 seconds
wall clock time: 42 minutes 19.21 seconds (2539.21 seconds total)