Starting phenix.real_space_refine
on Tue Mar 11 22:15:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gfz_29989/03_2025/8gfz_29989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gfz_29989/03_2025/8gfz_29989.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gfz_29989/03_2025/8gfz_29989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gfz_29989/03_2025/8gfz_29989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gfz_29989/03_2025/8gfz_29989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gfz_29989/03_2025/8gfz_29989.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.034
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    4311      2.51       5
     N    1154      2.21       5
     O    1231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6744
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1763
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 150
          Unresolved non-hydrogen angles: 182
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 107
    Chain: "B"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2433
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 111
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 88
          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': 3}
          Unresolved non-hydrogen planarities: 87
    Chain: "G"
      Number of atoms: 349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 349
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          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: 2147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2147
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 7, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 119
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 65
    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: 4.79, per 1000 atoms: 0.71
  Number of scatterers: 6744
  At special positions: 0
  Unit cell: (85.0346, 132.758, 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    1231      8.00
     N    1154      7.00
     C    4311      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 943.5 milliseconds
  

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      47.4% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.570A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 3.527A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.104A  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: 3.696A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.604A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.649A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.605A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 24
      removed outlier: 3.528A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.623A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.648A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 37 through 61
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.083A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.525A  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 104 through 137
      removed outlier: 3.598A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL R 126 " --> pdb=" O   GLU R 122 " (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: 3.606A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 238
      removed outlier: 3.785A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
      removed outlier: 3.560A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS R 235 " --> pdb=" O   GLN R 231 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU R 237 " --> pdb=" O   ILE R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.705A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.082A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.813A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.519A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.629A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.885A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.687A  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: 6.646A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.905A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.576A  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: 7.095A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.051A  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: 6.798A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.887A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.657A  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: 6.649A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.604A  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: 3.976A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    1008 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: 1.57

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1737
        1.33 -     1.45: 1331
        1.45 -     1.57: 3747
        1.57 -     1.69: 5
        1.69 -     1.81: 62
  Bond restraints: 6882
  Sorted by residual:
  bond pdb=" CA  GLU R 237 "
       pdb=" C   GLU R 237 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.039 1.43e-02 4.89e+03 7.26e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.75e+00
  bond pdb=" CA  GLU R 237 "
       pdb=" CB  GLU R 237 "
    ideal  model  delta    sigma   weight residual
    1.531  1.496  0.035 1.34e-02 5.57e+03 6.71e+00
  bond pdb=" N   LYS R 235 "
       pdb=" CA  LYS R 235 "
    ideal  model  delta    sigma   weight residual
    1.459  1.429  0.030 1.21e-02 6.83e+03 6.27e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 2.00e-02 2.50e+03 5.49e+00
  ... (remaining 6877 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 9274
        1.84 -     3.68: 88
        3.68 -     5.51: 23
        5.51 -     7.35: 2
        7.35 -     9.19: 1
  Bond angle restraints: 9388
  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  120.47   -9.19 1.09e+00 8.42e-01 7.11e+01
  angle pdb=" N   ASP R 234 "
        pdb=" CA  ASP R 234 "
        pdb=" C   ASP R 234 "
      ideal   model   delta    sigma   weight residual
     111.82  117.66   -5.84 1.16e+00 7.43e-01 2.53e+01
  angle pdb=" O   ILE R 233 "
        pdb=" C   ILE R 233 "
        pdb=" N   ASP R 234 "
      ideal   model   delta    sigma   weight residual
     121.87  117.29    4.58 9.70e-01 1.06e+00 2.23e+01
  angle pdb=" CA  ILE R 233 "
        pdb=" C   ILE R 233 "
        pdb=" N   ASP R 234 "
      ideal   model   delta    sigma   weight residual
     117.15  121.88   -4.73 1.14e+00 7.69e-01 1.72e+01
  angle pdb=" N   SER R 236 "
        pdb=" CA  SER R 236 "
        pdb=" CB  SER R 236 "
      ideal   model   delta    sigma   weight residual
     110.12  105.99    4.13 1.47e+00 4.63e-01 7.89e+00
  ... (remaining 9383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.07: 3895
       28.07 -    56.14: 108
       56.14 -    84.22: 9
       84.22 -   112.29: 0
      112.29 -   140.36: 3
  Dihedral angle restraints: 4015
    sinusoidal: 1417
      harmonic: 2598
  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  -35.77  140.36     1      2.00e+01 2.50e-03 4.25e+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
     303.79  175.06  128.74     1      2.00e+01 2.50e-03 3.90e+01
  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  -57.70  126.97     1      2.00e+01 2.50e-03 3.84e+01
  ... (remaining 4012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 797
       0.041 -    0.082: 244
       0.082 -    0.123: 61
       0.123 -    0.164: 3
       0.164 -    0.205: 1
  Chirality restraints: 1106
  Sorted by residual:
  chirality pdb=" CA  SER R 236 "
            pdb=" N   SER R 236 "
            pdb=" C   SER R 236 "
            pdb=" CB  SER R 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  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    2.55   -0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1103 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   1.60e-02 2.57e+00
        pdb=" C   ILE R 205 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO A 332 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 281 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   THR R 281 "    0.023 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 510
        2.74 -     3.28: 6307
        3.28 -     3.82: 10683
        3.82 -     4.36: 12368
        4.36 -     4.90: 22591
  Nonbonded interactions: 52459
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   TYR R 132 "
            pdb=" OG1 THR R 136 "
     model   vdw
     2.309 3.040
  ... (remaining 52454 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:             3.060
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.810
  Find NCS groups from input model:        0.050
  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:19.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
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   0.052   6882  Z= 0.189
  Angle     :  0.500   9.190   9388  Z= 0.287
  Chirality :  0.041   0.205   1106
  Planarity :  0.003   0.034   1177
  Dihedral  : 13.528 140.362   2324
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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:  0.72 (0.28), residues: 873
  helix:  1.44 (0.27), residues: 381
  sheet:  0.47 (0.41), residues: 165
  loop : -0.60 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.003   0.000   ARG R 239 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  386 MET cc_start: 0.8572 (ttm) cc_final: 0.8269 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 1.2737
  time to fit residues: 131.4593
Evaluate side-chains
  81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0770
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6738

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.119779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.094718 restraints weight = 8582.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.82
r_work: 0.2882 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.1076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6882  Z= 0.160
  Angle     :  0.487   5.552   9388  Z= 0.262
  Chirality :  0.041   0.131   1106
  Planarity :  0.003   0.027   1177
  Dihedral  :  8.624 140.355    979
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  7.51 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.28), residues: 873
  helix:  1.78 (0.27), residues: 391
  sheet:  0.56 (0.39), residues: 171
  loop : -0.57 (0.33), residues: 311

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   0.013   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.002   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.793 
Fit side-chains
REVERT: R  188 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7343 (mm-30)
REVERT: R  231 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7767 (tt0)
REVERT: R  239 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8087 (ptt180)
  outliers start: 8
  outliers final: 2
  residues processed: 94
  average time/residue: 1.3124
  time to fit residues: 129.6810
Evaluate side-chains
  88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain R residue  239 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.117312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.092065 restraints weight = 8722.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 1.84
r_work: 0.2838 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6882  Z= 0.224
  Angle     :  0.509   5.525   9388  Z= 0.271
  Chirality :  0.042   0.132   1106
  Planarity :  0.003   0.034   1177
  Dihedral  :  8.472 140.704    979
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.66 %
    Favored  : 88.44 %
  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:  1.12 (0.29), residues: 873
  helix:  1.84 (0.27), residues: 390
  sheet:  0.74 (0.40), residues: 164
  loop : -0.60 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.003   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.785 
Fit side-chains
REVERT: B  226 GLU cc_start: 0.7660 (pt0) cc_final: 0.7427 (pt0)
REVERT: B  303 ASP cc_start: 0.8611 (p0) cc_final: 0.8283 (p0)
REVERT: R   79 ASP cc_start: 0.8519 (m-30) cc_final: 0.8144 (m-30)
REVERT: R  188 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: R  231 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8038 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 91
  average time/residue: 1.3487
  time to fit residues: 129.1093
Evaluate side-chains
  85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.118072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.092658 restraints weight = 8839.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.85
r_work: 0.2840 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6882  Z= 0.194
  Angle     :  0.485   5.482   9388  Z= 0.259
  Chirality :  0.041   0.130   1106
  Planarity :  0.003   0.034   1177
  Dihedral  :  8.321 139.935    979
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.01 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.15 (0.29), residues: 873
  helix:  1.91 (0.27), residues: 390
  sheet:  0.80 (0.40), residues: 164
  loop : -0.68 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.002   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.703 
Fit side-chains
REVERT: B  303 ASP cc_start: 0.8541 (p0) cc_final: 0.8191 (p0)
REVERT: R   79 ASP cc_start: 0.8433 (m-30) cc_final: 0.8035 (m-30)
REVERT: R  188 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7379 (mm-30)
REVERT: R  231 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: R  239 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8038 (ptt180)
  outliers start: 14
  outliers final: 5
  residues processed: 93
  average time/residue: 1.2279
  time to fit residues: 120.2188
Evaluate side-chains
  83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  239 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0050
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.093202 restraints weight = 8694.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 1.83
r_work: 0.2855 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6882  Z= 0.162
  Angle     :  0.465   5.496   9388  Z= 0.250
  Chirality :  0.041   0.129   1106
  Planarity :  0.003   0.033   1177
  Dihedral  :  8.099 135.225    979
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.06 %
    Favored  : 85.44 %
  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:  1.28 (0.29), residues: 873
  helix:  2.05 (0.27), residues: 390
  sheet:  0.87 (0.40), residues: 164
  loop : -0.69 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 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   0.002   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.7942 (tttt) cc_final: 0.7666 (ttmm)
REVERT: B  303 ASP cc_start: 0.8488 (p0) cc_final: 0.8136 (p0)
REVERT: R   79 ASP cc_start: 0.8455 (m-30) cc_final: 0.8069 (m-30)
REVERT: R  231 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7774 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 85
  average time/residue: 1.3146
  time to fit residues: 117.4514
Evaluate side-chains
  80 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  146 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.117105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.091762 restraints weight = 8768.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.84
r_work: 0.2838 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6882  Z= 0.202
  Angle     :  0.488   5.606   9388  Z= 0.262
  Chirality :  0.042   0.132   1106
  Planarity :  0.003   0.035   1177
  Dihedral  :  8.048 133.496    979
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.36 %
    Favored  : 84.38 %
  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:  1.24 (0.29), residues: 873
  helix:  2.02 (0.27), residues: 390
  sheet:  0.86 (0.41), residues: 164
  loop : -0.71 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.002   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.8011 (tttt) cc_final: 0.7748 (ttmm)
REVERT: A   34 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8078 (tttp)
REVERT: B  303 ASP cc_start: 0.8536 (p0) cc_final: 0.8201 (p0)
REVERT: R   79 ASP cc_start: 0.8501 (m-30) cc_final: 0.8128 (m-30)
REVERT: R  103 ASN cc_start: 0.8753 (m-40) cc_final: 0.8501 (m110)
REVERT: R  188 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7424 (mm-30)
REVERT: R  231 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7827 (tm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 89
  average time/residue: 1.3911
  time to fit residues: 129.8749
Evaluate side-chains
  86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  146 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    0.0770
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3324 r_free = 0.3324 target = 0.120110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.094789 restraints weight = 8712.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.84
r_work: 0.2871 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6882  Z= 0.138
  Angle     :  0.451   5.561   9388  Z= 0.242
  Chirality :  0.040   0.128   1106
  Planarity :  0.003   0.030   1177
  Dihedral  :  7.779 129.670    979
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.66 %
    Favored  : 84.38 %
  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:  1.42 (0.29), residues: 873
  helix:  2.20 (0.27), residues: 390
  sheet:  0.86 (0.40), residues: 168
  loop : -0.64 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.007   0.001   TYR R 209 
 ARG   0.004   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.7811 (tttt) cc_final: 0.7564 (ttmm)
REVERT: A   34 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7983 (tttp)
REVERT: A  268 GLU cc_start: 0.7658 (tp30) cc_final: 0.6956 (tt0)
REVERT: B  303 ASP cc_start: 0.8462 (p0) cc_final: 0.8162 (p0)
REVERT: R   79 ASP cc_start: 0.8494 (m-30) cc_final: 0.8046 (m-30)
REVERT: R  228 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7393 (ttm110)
REVERT: R  231 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7743 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 88
  average time/residue: 1.2563
  time to fit residues: 116.4876
Evaluate side-chains
  83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  302 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3306 r_free = 0.3306 target = 0.118619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.093232 restraints weight = 8756.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.84
r_work: 0.2850 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6882  Z= 0.174
  Angle     :  0.480   5.582   9388  Z= 0.257
  Chirality :  0.042   0.272   1106
  Planarity :  0.003   0.033   1177
  Dihedral  :  7.737 127.424    979
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.26 %
    Favored  : 83.93 %
  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:  1.42 (0.29), residues: 873
  helix:  2.22 (0.27), residues: 390
  sheet:  0.81 (0.40), residues: 169
  loop : -0.63 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.005   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.7816 (tttt) cc_final: 0.7566 (ttmm)
REVERT: A   34 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7963 (tttp)
REVERT: B  303 ASP cc_start: 0.8482 (p0) cc_final: 0.8147 (p0)
REVERT: R  228 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7380 (ttm110)
REVERT: R  231 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7749 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 86
  average time/residue: 1.2581
  time to fit residues: 113.8174
Evaluate side-chains
  84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  302 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.0050
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3328 r_free = 0.3328 target = 0.120302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.094978 restraints weight = 8771.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.82
r_work: 0.2869 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6882  Z= 0.147
  Angle     :  0.465   5.527   9388  Z= 0.249
  Chirality :  0.041   0.140   1106
  Planarity :  0.003   0.030   1177
  Dihedral  :  7.535 123.348    979
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.26 %
    Favored  : 83.78 %
  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:  1.45 (0.29), residues: 873
  helix:  2.25 (0.27), residues: 390
  sheet:  0.81 (0.40), residues: 168
  loop : -0.60 (0.33), residues: 315

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   0.007   0.001   TYR A 339 
 ARG   0.005   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.7819 (tttt) cc_final: 0.7580 (ttmm)
REVERT: A   34 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7987 (tttp)
REVERT: A  268 GLU cc_start: 0.7639 (tp30) cc_final: 0.6919 (tt0)
REVERT: B  303 ASP cc_start: 0.8459 (p0) cc_final: 0.8158 (p0)
REVERT: R   79 ASP cc_start: 0.8467 (m-30) cc_final: 0.8127 (m-30)
REVERT: R  228 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7415 (ttm110)
REVERT: R  231 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7742 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 88
  average time/residue: 1.2380
  time to fit residues: 115.0294
Evaluate side-chains
  88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  302 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3303 r_free = 0.3303 target = 0.118390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.092859 restraints weight = 8903.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.85
r_work: 0.2842 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6882  Z= 0.184
  Angle     :  0.489   5.520   9388  Z= 0.262
  Chirality :  0.042   0.253   1106
  Planarity :  0.003   0.034   1177
  Dihedral  :  7.478 120.328    979
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.41 %
    Favored  : 83.78 %
  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:  1.40 (0.29), residues: 873
  helix:  2.23 (0.27), residues: 390
  sheet:  0.81 (0.41), residues: 164
  loop : -0.65 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.006   0.000   ARG B 219 

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   25 LYS cc_start: 0.7820 (tttt) cc_final: 0.7572 (ttmm)
REVERT: A   34 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7946 (tttp)
REVERT: A  221 MET cc_start: 0.8204 (ttp) cc_final: 0.7859 (ttp)
REVERT: B  303 ASP cc_start: 0.8477 (p0) cc_final: 0.8159 (p0)
REVERT: R   79 ASP cc_start: 0.8468 (m-30) cc_final: 0.8175 (m-30)
REVERT: R  228 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7377 (ttm110)
REVERT: R  231 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7781 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 88
  average time/residue: 1.2367
  time to fit residues: 114.6860
Evaluate side-chains
  87 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  302 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3319 r_free = 0.3319 target = 0.119552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.094145 restraints weight = 8811.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 1.84
r_work: 0.2857 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6882  Z= 0.165
  Angle     :  0.478   5.483   9388  Z= 0.255
  Chirality :  0.041   0.145   1106
  Planarity :  0.003   0.031   1177
  Dihedral  :  7.327 116.399    979
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.11 %
    Favored  : 83.93 %
  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:  1.42 (0.29), residues: 873
  helix:  2.23 (0.27), residues: 390
  sheet:  0.66 (0.39), residues: 174
  loop : -0.55 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.005   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4920.82 seconds
wall clock time: 84 minutes 31.39 seconds (5071.39 seconds total)