Starting phenix.real_space_refine
on Tue Feb 11 23:03:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gg0_29990/02_2025/8gg0_29990.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gg0_29990/02_2025/8gg0_29990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gg0_29990/02_2025/8gg0_29990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gg0_29990/02_2025/8gg0_29990.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gg0_29990/02_2025/8gg0_29990.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gg0_29990/02_2025/8gg0_29990.cif"
  }
  resolution = 2.9
  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=   0.036
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      45      5.16       5
     C    4316      2.51       5
     N    1155      2.21       5
     O    1226      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: 6745
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1748
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 180
          Unresolved non-hydrogen angles: 217
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 127
    Chain: "B"
      Number of atoms: 2427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2427
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 141
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 90
    Chain: "G"
      Number of atoms: 347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 347
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 2171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2171
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 76
    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: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 20
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 5}
          Link IDs: {None: 5}
  Time building chain proxies: 4.74, per 1000 atoms: 0.70
  Number of scatterers: 6745
  At special positions: 0
  Unit cell: (83.2992, 134.493, 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      45     16.00
     P       3     15.00
     O    1226      8.00
     N    1155      7.00
     C    4316      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: 1.58
  Conformation dependent library (CDL) restraints added in 980.8 milliseconds
  

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      48.5% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.774A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.807A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 3.716A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.553A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.743A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.968A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 24
      removed outlier: 3.542A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.563A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.641A  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 33 through 61
      removed outlier: 3.507A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
      removed outlier: 3.777A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 62 through 65'
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.081A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.685A  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 101 through 137
      removed outlier: 4.337A  pdb=" N   TRP R 105 " --> pdb=" O   PHE R 101 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.675A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
      removed outlier: 3.513A  pdb=" N   GLU R 187 " --> pdb=" O   ASN R 183 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 237
      removed outlier: 3.679A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
      removed outlier: 3.542A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS R 232 " --> pdb=" O   ARG R 228 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE R 233 " --> pdb=" O   GLN R 229 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASP R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.748A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.015A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.820A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 321
      No H-bonds generated for 'chain 'R' and resid 319 through 321'
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.906A  pdb=" N   ALA R 335 " --> pdb=" O   ASP R 331 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN R 337 " --> pdb=" O   ARG R 333 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.216A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.638A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.639A  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 51
      removed outlier: 6.691A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.531A  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: 4.052A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.604A  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 105
      removed outlier: 7.119A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.832A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.857A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.637A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.905A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    334 hydrogen bonds defined for protein.
    966 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: 1.85

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1075
        1.32 -     1.44: 1936
        1.44 -     1.57: 3806
        1.57 -     1.69: 6
        1.69 -     1.81: 62
  Bond restraints: 6885
  Sorted by residual:
  bond pdb=" C   ILE R 233 "
       pdb=" O   ILE R 233 "
    ideal  model  delta    sigma   weight residual
    1.237  1.195  0.042 1.17e-02 7.31e+03 1.29e+01
  bond pdb=" C   LYS R 232 "
       pdb=" O   LYS R 232 "
    ideal  model  delta    sigma   weight residual
    1.237  1.204  0.033 1.17e-02 7.31e+03 7.73e+00
  bond pdb=" C   LEU R 230 "
       pdb=" N   GLN R 231 "
    ideal  model  delta    sigma   weight residual
    1.335  1.301  0.034 1.31e-02 5.83e+03 6.78e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.38e+00
  bond pdb=" CA  LYS R 235 "
       pdb=" C   LYS R 235 "
    ideal  model  delta    sigma   weight residual
    1.524  1.494  0.031 1.24e-02 6.50e+03 6.06e+00
  ... (remaining 6880 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 9192
        1.35 -     2.69: 154
        2.69 -     4.04: 32
        4.04 -     5.38: 15
        5.38 -     6.73: 6
  Bond angle restraints: 9399
  Sorted by residual:
  angle pdb=" N   SER R 236 "
        pdb=" CA  SER R 236 "
        pdb=" C   SER R 236 "
      ideal   model   delta    sigma   weight residual
     111.28  118.01   -6.73 1.09e+00 8.42e-01 3.81e+01
  angle pdb=" N   LYS R 232 "
        pdb=" CA  LYS R 232 "
        pdb=" C   LYS R 232 "
      ideal   model   delta    sigma   weight residual
     111.28  117.90   -6.62 1.09e+00 8.42e-01 3.69e+01
  angle pdb=" O   LEU R 230 "
        pdb=" C   LEU R 230 "
        pdb=" N   GLN R 231 "
      ideal   model   delta    sigma   weight residual
     122.12  116.45    5.67 1.06e+00 8.90e-01 2.86e+01
  angle pdb=" CA  LEU R 230 "
        pdb=" C   LEU R 230 "
        pdb=" N   GLN R 231 "
      ideal   model   delta    sigma   weight residual
     117.30  123.05   -5.75 1.16e+00 7.43e-01 2.46e+01
  angle pdb=" N   ASP R 234 "
        pdb=" CA  ASP R 234 "
        pdb=" C   ASP R 234 "
      ideal   model   delta    sigma   weight residual
     113.28  117.92   -4.64 1.22e+00 6.72e-01 1.45e+01
  ... (remaining 9394 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.29: 3885
       28.29 -    56.58: 110
       56.58 -    84.87: 11
       84.87 -   113.17: 1
      113.17 -   141.46: 1
  Dihedral angle restraints: 4008
    sinusoidal: 1393
      harmonic: 2615
  Sorted by residual:
  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  -36.86  141.46     1      2.00e+01 2.50e-03 4.28e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21 -159.06  102.85     1      2.00e+01 2.50e-03 2.93e+01
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.74  -24.26     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 4005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 724
       0.034 -    0.068: 278
       0.068 -    0.103: 83
       0.103 -    0.137: 24
       0.137 -    0.171: 3
  Chirality restraints: 1112
  Sorted by residual:
  chirality pdb=" CA  LYS R 232 "
            pdb=" N   LYS R 232 "
            pdb=" C   LYS R 232 "
            pdb=" CB  LYS R 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.32e-01
  chirality pdb=" CA  ASP R 234 "
            pdb=" N   ASP R 234 "
            pdb=" C   ASP R 234 "
            pdb=" CB  ASP R 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.76e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.11e-01
  ... (remaining 1109 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   ILE R 205 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 230 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.59e+00
        pdb=" C   LEU R 230 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU R 230 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLN R 231 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 281 "   -0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" C   THR R 281 "    0.020 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 856
        2.75 -     3.29: 6107
        3.29 -     3.83: 10610
        3.83 -     4.36: 12314
        4.36 -     4.90: 22571
  Nonbonded interactions: 52458
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   TYR R 132 "
            pdb=" OG1 THR R 136 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD2 ASP A 343 "
            pdb=" NH2 ARG R 239 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   SER R 137 "
            pdb=" OG  SER R 137 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OD1 ASN A 239 "
            pdb=" NZ  LYS B  57 "
     model   vdw
     2.348 3.120
  ... (remaining 52453 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 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:             2.120
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.810
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
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      :  0.003   0.051   6885  Z= 0.209
  Angle     :  0.512   6.731   9399  Z= 0.297
  Chirality :  0.041   0.171   1112
  Planarity :  0.003   0.028   1177
  Dihedral  : 13.395 141.458   2307
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.54 (0.28), residues: 881
  helix:  1.23 (0.26), residues: 388
  sheet:  0.42 (0.41), residues: 160
  loop : -0.63 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.002   0.000   ARG R 228 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.724 
Fit side-chains
REVERT: B  153 ASP cc_start: 0.7488 (t70) cc_final: 0.7211 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 1.1225
  time to fit residues: 103.5220
Evaluate side-chains
  74 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0670
   chunk 36 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
B 175 GLN
R 241 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.134949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.107681 restraints weight = 8681.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.26
r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   6885  Z= 0.184
  Angle     :  0.495   5.793   9399  Z= 0.265
  Chirality :  0.041   0.129   1112
  Planarity :  0.003   0.029   1177
  Dihedral  :  8.232 141.285    985
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  6.82 %
    Favored  : 91.67 %
  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:  1.02 (0.28), residues: 881
  helix:  1.78 (0.27), residues: 390
  sheet:  0.47 (0.42), residues: 159
  loop : -0.51 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.002   0.000   ARG R 228 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8118 (tp40) cc_final: 0.7840 (mm-40)
REVERT: B  153 ASP cc_start: 0.7804 (t70) cc_final: 0.7499 (t70)
REVERT: R   82 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6729 (tpp)
  outliers start: 10
  outliers final: 4
  residues processed: 90
  average time/residue: 1.1974
  time to fit residues: 113.7745
Evaluate side-chains
  81 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 236 GLN
B 175 GLN
R  51 ASN
R  65 GLN
R 241 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.108309 restraints weight = 8834.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.25
r_work: 0.3128 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6885  Z= 0.173
  Angle     :  0.474   5.805   9399  Z= 0.253
  Chirality :  0.041   0.130   1112
  Planarity :  0.003   0.030   1177
  Dihedral  :  8.162 141.155    985
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.85 %
    Favored  : 88.33 %
  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:  1.18 (0.29), residues: 881
  helix:  1.98 (0.27), residues: 391
  sheet:  0.55 (0.41), residues: 159
  loop : -0.53 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.002   0.000   ARG R 228 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8140 (tp40) cc_final: 0.7861 (mm-40)
REVERT: B  153 ASP cc_start: 0.7796 (t70) cc_final: 0.7423 (t70)
REVERT: B  262 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8582 (ttm)
REVERT: R   82 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6695 (tpp)
  outliers start: 12
  outliers final: 5
  residues processed: 85
  average time/residue: 1.2607
  time to fit residues: 113.0996
Evaluate side-chains
  86 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 236 GLN
B 175 GLN
R  51 ASN
R 241 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.134679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.107542 restraints weight = 8850.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.26
r_work: 0.3107 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6885  Z= 0.183
  Angle     :  0.477   5.817   9399  Z= 0.254
  Chirality :  0.041   0.132   1112
  Planarity :  0.003   0.033   1177
  Dihedral  :  8.164 141.207    985
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.18 %
    Favored  : 85.45 %
  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:  1.26 (0.29), residues: 881
  helix:  2.07 (0.27), residues: 389
  sheet:  0.66 (0.41), residues: 159
  loop : -0.55 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 336 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8199 (tp40) cc_final: 0.7926 (mm-40)
REVERT: A  368 ASP cc_start: 0.8081 (m-30) cc_final: 0.7705 (m-30)
REVERT: B  153 ASP cc_start: 0.7826 (t70) cc_final: 0.7437 (t70)
REVERT: B  262 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8549 (ttm)
REVERT: R   82 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6684 (tpp)
  outliers start: 9
  outliers final: 6
  residues processed: 85
  average time/residue: 1.2442
  time to fit residues: 111.4394
Evaluate side-chains
  86 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0470
   chunk 73 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 236 GLN
B 175 GLN
R  51 ASN
R 241 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.135239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.108438 restraints weight = 8778.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.22
r_work: 0.3122 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6885  Z= 0.162
  Angle     :  0.461   5.799   9399  Z= 0.246
  Chirality :  0.041   0.138   1112
  Planarity :  0.003   0.033   1177
  Dihedral  :  8.105 141.011    985
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.88 %
    Favored  : 85.00 %
  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:  1.35 (0.29), residues: 881
  helix:  2.13 (0.27), residues: 391
  sheet:  0.80 (0.41), residues: 158
  loop : -0.54 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 336 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.785 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8174 (tp40) cc_final: 0.7911 (mm-40)
REVERT: A  368 ASP cc_start: 0.8053 (m-30) cc_final: 0.7709 (m-30)
REVERT: B  153 ASP cc_start: 0.7807 (t70) cc_final: 0.7414 (t70)
REVERT: B  234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8945 (m-80)
REVERT: B  262 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (ttm)
REVERT: R   82 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6719 (tpp)
  outliers start: 14
  outliers final: 7
  residues processed: 86
  average time/residue: 1.2382
  time to fit residues: 112.5278
Evaluate side-chains
  88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0670
   chunk 58 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
B 175 GLN
B 237 ASN
R  51 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.108720 restraints weight = 8830.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.25
r_work: 0.3122 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6885  Z= 0.153
  Angle     :  0.459   5.796   9399  Z= 0.245
  Chirality :  0.041   0.145   1112
  Planarity :  0.003   0.032   1177
  Dihedral  :  8.038 140.643    985
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.24 %
    Favored  : 83.94 %
  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:  1.41 (0.29), residues: 881
  helix:  2.18 (0.27), residues: 391
  sheet:  0.71 (0.40), residues: 164
  loop : -0.47 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 336 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8165 (tp40) cc_final: 0.7909 (mm-40)
REVERT: A  368 ASP cc_start: 0.8012 (m-30) cc_final: 0.7675 (m-30)
REVERT: B  153 ASP cc_start: 0.7827 (t70) cc_final: 0.7435 (t70)
REVERT: B  234 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8961 (m-80)
REVERT: B  262 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (ttm)
REVERT: R   52 VAL cc_start: 0.8041 (t) cc_final: 0.7781 (m)
REVERT: R   82 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6710 (tpp)
  outliers start: 12
  outliers final: 6
  residues processed: 89
  average time/residue: 1.1909
  time to fit residues: 112.1895
Evaluate side-chains
  85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.134119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.107312 restraints weight = 8787.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.22
r_work: 0.3104 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6885  Z= 0.187
  Angle     :  0.485   5.844   9399  Z= 0.258
  Chirality :  0.041   0.153   1112
  Planarity :  0.003   0.034   1177
  Dihedral  :  8.108 140.915    985
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.15 %
    Favored  : 83.18 %
  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:  1.35 (0.29), residues: 881
  helix:  2.15 (0.27), residues: 391
  sheet:  0.65 (0.40), residues: 164
  loop : -0.52 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  63 
 HIS   0.012   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 336 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8170 (tp40) cc_final: 0.7914 (mm-40)
REVERT: A  368 ASP cc_start: 0.8037 (m-30) cc_final: 0.7679 (m-30)
REVERT: B   16 ASN cc_start: 0.7304 (m-40) cc_final: 0.6660 (m110)
REVERT: B  153 ASP cc_start: 0.7896 (t70) cc_final: 0.7515 (t70)
REVERT: B  262 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8535 (ttm)
REVERT: R   82 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6707 (tpp)
  outliers start: 11
  outliers final: 7
  residues processed: 84
  average time/residue: 1.2470
  time to fit residues: 110.5424
Evaluate side-chains
  88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0000
   chunk 20 optimal weight:    4.9990
   chunk 15 optimal weight:    0.2980
   chunk 33 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.2582

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.112528 restraints weight = 8782.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.23
r_work: 0.3177 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6885  Z= 0.106
  Angle     :  0.424   5.721   9399  Z= 0.226
  Chirality :  0.040   0.155   1112
  Planarity :  0.003   0.028   1177
  Dihedral  :  7.795 139.102    985
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.61 %
    Favored  : 82.88 %
  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:  1.55 (0.29), residues: 881
  helix:  2.32 (0.27), residues: 394
  sheet:  0.76 (0.41), residues: 160
  loop : -0.42 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.001   0.000   ARG B 251 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8174 (tp40) cc_final: 0.7915 (mm-40)
REVERT: A  368 ASP cc_start: 0.7922 (m-30) cc_final: 0.7642 (m-30)
REVERT: B  153 ASP cc_start: 0.7757 (t70) cc_final: 0.7383 (t70)
REVERT: R   52 VAL cc_start: 0.7976 (t) cc_final: 0.7728 (m)
REVERT: R   82 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6845 (tpp)
REVERT: R  130 ASP cc_start: 0.8785 (t70) cc_final: 0.8577 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 89
  average time/residue: 1.1789
  time to fit residues: 110.8953
Evaluate side-chains
  85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0170
   chunk 86 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.7818

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
B 237 ASN
R  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.108726 restraints weight = 8935.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.24
r_work: 0.3125 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6885  Z= 0.175
  Angle     :  0.467   5.852   9399  Z= 0.249
  Chirality :  0.041   0.158   1112
  Planarity :  0.003   0.031   1177
  Dihedral  :  7.851 139.409    985
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.21 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.55 (0.29), residues: 881
  helix:  2.32 (0.27), residues: 393
  sheet:  0.67 (0.40), residues: 164
  loop : -0.39 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  63 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.002   0.000   ARG R 333 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8172 (tp40) cc_final: 0.7919 (mm-40)
REVERT: A  368 ASP cc_start: 0.8048 (m-30) cc_final: 0.7735 (m-30)
REVERT: B   16 ASN cc_start: 0.7280 (m-40) cc_final: 0.6662 (m110)
REVERT: B  153 ASP cc_start: 0.7903 (t70) cc_final: 0.7538 (t70)
REVERT: R   52 VAL cc_start: 0.7937 (t) cc_final: 0.7694 (m)
REVERT: R   82 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6714 (tpp)
  outliers start: 10
  outliers final: 6
  residues processed: 87
  average time/residue: 1.1929
  time to fit residues: 109.7085
Evaluate side-chains
  90 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107672 restraints weight = 8942.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.27
r_work: 0.3112 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6885  Z= 0.179
  Angle     :  0.477   5.851   9399  Z= 0.254
  Chirality :  0.041   0.158   1112
  Planarity :  0.003   0.034   1177
  Dihedral  :  7.856 139.733    985
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.21 %
    Favored  : 82.42 %
  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:  1.49 (0.29), residues: 881
  helix:  2.28 (0.27), residues: 392
  sheet:  0.64 (0.40), residues: 164
  loop : -0.43 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  63 
 HIS   0.011   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.002   0.000   ARG R 333 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8180 (tp40) cc_final: 0.7919 (mm-40)
REVERT: A  368 ASP cc_start: 0.8077 (m-30) cc_final: 0.7844 (m-30)
REVERT: B   16 ASN cc_start: 0.7292 (m-40) cc_final: 0.6650 (m110)
REVERT: B  153 ASP cc_start: 0.7949 (t70) cc_final: 0.7557 (t70)
REVERT: R   52 VAL cc_start: 0.8001 (t) cc_final: 0.7734 (m)
REVERT: R   82 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6721 (tpp)
  outliers start: 9
  outliers final: 6
  residues processed: 85
  average time/residue: 1.2617
  time to fit residues: 113.1218
Evaluate side-chains
  88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  184 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.134967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.107921 restraints weight = 8871.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.23
r_work: 0.3115 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6885  Z= 0.172
  Angle     :  0.471   5.807   9399  Z= 0.252
  Chirality :  0.041   0.159   1112
  Planarity :  0.003   0.033   1177
  Dihedral  :  7.779 139.903    985
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.21 %
    Favored  : 82.58 %
  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:  1.48 (0.29), residues: 881
  helix:  2.28 (0.27), residues: 392
  sheet:  0.64 (0.40), residues: 164
  loop : -0.43 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.011   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.001   0.000   ARG B 283 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4643.32 seconds
wall clock time: 82 minutes 30.42 seconds (4950.42 seconds total)