Starting phenix.real_space_refine
on Sun Apr 27 23:27:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gfy_29988/04_2025/8gfy_29988.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gfy_29988/04_2025/8gfy_29988.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/8gfy_29988/04_2025/8gfy_29988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gfy_29988/04_2025/8gfy_29988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gfy_29988/04_2025/8gfy_29988.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gfy_29988/04_2025/8gfy_29988.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=   0.035
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      42      5.16       5
     C    4278      2.51       5
     N    1138      2.21       5
     O    1209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6670
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1742
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 5, 'TRANS': 224}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 170
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 120
    Chain: "B"
      Number of atoms: 2426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2426
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 90
    Chain: "G"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 348
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 1
          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: 2103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2103
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 7, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 116
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 94
    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: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 19
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 4}
          Link IDs: {None: 4}
  Time building chain proxies: 5.93, per 1000 atoms: 0.89
  Number of scatterers: 6670
  At special positions: 0
  Unit cell: (83.2992, 132.758, 100.653, 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      42     16.00
     P       3     15.00
     O    1209      8.00
     N    1138      7.00
     C    4278      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: 1.92
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  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:
      28 helices and 8 sheets defined
      48.5% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.613A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.506A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 3.665A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.558A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.666A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.500A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 26
      removed outlier: 3.767A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.786A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.534A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (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 62 through 65
      removed outlier: 3.855A  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: 4.060A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.400A  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 103 through 137
      removed outlier: 3.649A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL R 126 " --> pdb=" O   GLU R 122 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.584A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 163
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.623A  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: 3.824A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
      removed outlier: 3.575A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS R 232 " --> pdb=" O   ARG R 228 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE R 233 " --> pdb=" O   GLN R 229 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 239 through 241
      No H-bonds generated for 'chain 'R' and resid 239 through 241'
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.742A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.174A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.804A  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: 4.542A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.696A  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: 6.622A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.930A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.107A  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: 7.151A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.874A  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: 6.859A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.122A  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: 6.911A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.663A  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: 6.650A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.868A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    343 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.96

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2141
        1.34 -     1.46: 1494
        1.46 -     1.58: 3114
        1.58 -     1.69: 5
        1.69 -     1.81: 57
  Bond restraints: 6811
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 7.00e+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 5.61e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.20e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 2.00e-02 2.50e+03 4.34e+00
  bond pdb=" CAE G1I R 501 "
       pdb=" CAG G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.506  1.538 -0.032 2.00e-02 2.50e+03 2.62e+00
  ... (remaining 6806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 9104
        1.23 -     2.47: 152
        2.47 -     3.70: 30
        3.70 -     4.93: 12
        4.93 -     6.17: 6
  Bond angle restraints: 9304
  Sorted by residual:
  angle pdb=" N   ARG B 197 "
        pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
      ideal   model   delta    sigma   weight residual
     114.56  109.97    4.59 1.27e+00 6.20e-01 1.31e+01
  angle pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
        pdb=" N   LEU B 198 "
      ideal   model   delta    sigma   weight residual
     119.26  116.45    2.81 1.14e+00 7.69e-01 6.08e+00
  angle pdb=" N   PHE R 208 "
        pdb=" CA  PHE R 208 "
        pdb=" C   PHE R 208 "
      ideal   model   delta    sigma   weight residual
     112.72  115.65   -2.93 1.28e+00 6.10e-01 5.26e+00
  angle pdb=" C2' GTP A 401 "
        pdb=" C3' GTP A 401 "
        pdb=" C4' GTP A 401 "
      ideal   model   delta    sigma   weight residual
     111.00  104.83    6.17 3.00e+00 1.11e-01 4.23e+00
  angle pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
        pdb=" O   ARG B 197 "
      ideal   model   delta    sigma   weight residual
     118.55  120.76   -2.21 1.14e+00 7.69e-01 3.77e+00
  ... (remaining 9299 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.59: 3845
       28.59 -    57.17: 97
       57.17 -    85.76: 8
       85.76 -   114.34: 0
      114.34 -   142.93: 2
  Dihedral angle restraints: 3952
    sinusoidal: 1354
      harmonic: 2598
  Sorted by residual:
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -147.80 -142.93     1      2.00e+01 2.50e-03 4.31e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   -9.93  114.52     1      2.00e+01 2.50e-03 3.40e+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 -160.65  -19.35     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 3949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 732
       0.034 -    0.068: 271
       0.068 -    0.102: 75
       0.102 -    0.136: 25
       0.136 -    0.170: 1
  Chirality restraints: 1104
  Sorted by residual:
  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    2.57   -0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  VAL B 112 "
            pdb=" N   VAL B 112 "
            pdb=" C   VAL B 112 "
            pdb=" CB  VAL B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-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   -0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 1101 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO A 332 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "    0.008 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" C   ILE R 205 "   -0.026 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=" CA  THR R 281 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   THR R 281 "    0.020 2.00e-02 2.50e+03
        pdb=" O   THR R 281 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   PHE R 282 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 976
        2.76 -     3.29: 6033
        3.29 -     3.83: 10567
        3.83 -     4.36: 12046
        4.36 -     4.90: 22332
  Nonbonded interactions: 51954
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OH  TYR R 326 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   TYR R 132 "
            pdb=" OG1 THR R 136 "
     model   vdw
     2.322 3.040
  ... (remaining 51949 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:             71.620
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     29.890
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:22.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  124.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
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   0.053   6812  Z= 0.122
  Angle     :  0.464   6.167   9306  Z= 0.248
  Chirality :  0.040   0.170   1104
  Planarity :  0.003   0.048   1164
  Dihedral  : 12.901 142.927   2261
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 873
  helix:  1.49 (0.27), residues: 389
  sheet:  0.59 (0.40), residues: 165
  loop : -0.53 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.002   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19437 (  343)
  hydrogen bonds       : angle       6.19752 (  999)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       1.16074 (    2)
  covalent geometry    : bond        0.00250 ( 6811)
  covalent geometry    : angle       0.46372 ( 9304)

*********************** 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
  97 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.842 
Fit side-chains
  outliers start: 0
  outliers final: 1
  residues processed: 97
  average time/residue: 1.6064
  time to fit residues: 164.3543
Evaluate side-chains
  83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.118315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.095382 restraints weight = 8845.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.68
r_work: 0.2892 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6812  Z= 0.138
  Angle     :  0.510   6.277   9306  Z= 0.273
  Chirality :  0.042   0.192   1104
  Planarity :  0.003   0.042   1164
  Dihedral  :  8.152 144.491    978
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.85 %
    Favored  : 89.91 %
  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:  0.90 (0.28), residues: 873
  helix:  1.63 (0.27), residues: 391
  sheet:  0.56 (0.42), residues: 159
  loop : -0.62 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 297 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.002   0.000   ARG A 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05540 (  343)
  hydrogen bonds       : angle       4.51190 (  999)
  SS BOND              : bond        0.00294 (    1)
  SS BOND              : angle       1.48459 (    2)
  covalent geometry    : bond        0.00315 ( 6811)
  covalent geometry    : angle       0.50919 ( 9304)

*********************** 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
  92 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  330 GLU cc_start: 0.7438 (tt0) cc_final: 0.7035 (tt0)
REVERT: B  262 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8619 (ttp)
  outliers start: 8
  outliers final: 4
  residues processed: 87
  average time/residue: 1.5264
  time to fit residues: 141.3027
Evaluate side-chains
  81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  262 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0570
   chunk 70 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.096786 restraints weight = 8937.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.72
r_work: 0.2926 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6812  Z= 0.104
  Angle     :  0.452   6.237   9306  Z= 0.242
  Chirality :  0.040   0.133   1104
  Planarity :  0.003   0.037   1164
  Dihedral  :  7.601 145.956    976
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 10.71 %
    Favored  : 87.42 %
  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:  1.07 (0.28), residues: 873
  helix:  1.79 (0.27), residues: 392
  sheet:  0.66 (0.42), residues: 159
  loop : -0.58 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.001   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04451 (  343)
  hydrogen bonds       : angle       4.24837 (  999)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       1.13999 (    2)
  covalent geometry    : bond        0.00224 ( 6811)
  covalent geometry    : angle       0.45151 ( 9304)

*********************** 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
  93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7969 (ttpt)
REVERT: A  330 GLU cc_start: 0.7255 (tt0) cc_final: 0.6767 (tt0)
REVERT: R   65 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8208 (mt0)
  outliers start: 12
  outliers final: 5
  residues processed: 84
  average time/residue: 1.3308
  time to fit residues: 118.6913
Evaluate side-chains
  84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain R residue   65 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.118997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.096052 restraints weight = 8988.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.69
r_work: 0.2936 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6812  Z= 0.171
  Angle     :  0.532   6.417   9306  Z= 0.282
  Chirality :  0.043   0.139   1104
  Planarity :  0.003   0.042   1164
  Dihedral  :  7.764 147.310    976
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.96 %
    Favored  : 85.71 %
  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:  0.93 (0.28), residues: 873
  helix:  1.64 (0.26), residues: 392
  sheet:  0.58 (0.41), residues: 165
  loop : -0.62 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  63 
 HIS   0.005   0.001   HIS R 178 
 PHE   0.014   0.002   PHE A 212 
 TYR   0.012   0.001   TYR R 132 
 ARG   0.001   0.000   ARG A 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05798 (  343)
  hydrogen bonds       : angle       4.35590 (  999)
  SS BOND              : bond        0.00469 (    1)
  SS BOND              : angle       1.95978 (    2)
  covalent geometry    : bond        0.00412 ( 6811)
  covalent geometry    : angle       0.53088 ( 9304)

*********************** 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
  94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  330 GLU cc_start: 0.7201 (tt0) cc_final: 0.6783 (tt0)
REVERT: B  234 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.7845 (m-80)
REVERT: R   65 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8273 (mt0)
  outliers start: 15
  outliers final: 7
  residues processed: 86
  average time/residue: 0.9967
  time to fit residues: 91.3310
Evaluate side-chains
  87 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   40 VAL
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 B residue  325 MET
Chi-restraints excluded: chain R residue   65 GLN
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  190 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 36 optimal weight:    0.1980
   chunk 55 optimal weight:    0.4980
   chunk 23 optimal weight:   20.0000
   chunk 13 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.123171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.100388 restraints weight = 8877.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.69
r_work: 0.2987 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6812  Z= 0.093
  Angle     :  0.443   6.184   9306  Z= 0.237
  Chirality :  0.040   0.133   1104
  Planarity :  0.003   0.031   1164
  Dihedral  :  7.598 147.576    976
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.35 %
    Favored  : 85.09 %
  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:  1.10 (0.28), residues: 873
  helix:  1.82 (0.27), residues: 391
  sheet:  0.75 (0.42), residues: 159
  loop : -0.62 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.001   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  343)
  hydrogen bonds       : angle       4.14685 (  999)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       1.02124 (    2)
  covalent geometry    : bond        0.00188 ( 6811)
  covalent geometry    : angle       0.44246 ( 9304)

*********************** 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
  91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  330 GLU cc_start: 0.7118 (tt0) cc_final: 0.6601 (tt0)
REVERT: B  175 GLN cc_start: 0.8224 (mm110) cc_final: 0.7996 (tp40)
REVERT: B  234 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8203 (m-80)
  outliers start: 10
  outliers final: 4
  residues processed: 86
  average time/residue: 1.0470
  time to fit residues: 95.6639
Evaluate side-chains
  85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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  234 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0570
   overall best weight:    0.7302

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
B 340 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 = 0.3376 r_free = 0.3376 target = 0.122226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.099379 restraints weight = 8826.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.69
r_work: 0.2974 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6812  Z= 0.106
  Angle     :  0.457   6.258   9306  Z= 0.244
  Chirality :  0.040   0.132   1104
  Planarity :  0.003   0.034   1164
  Dihedral  :  7.579 147.616    976
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.13 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.28), residues: 873
  helix:  1.82 (0.27), residues: 394
  sheet:  0.78 (0.42), residues: 159
  loop : -0.55 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.010   0.001   PHE R 289 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  343)
  hydrogen bonds       : angle       4.07558 (  999)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       1.21195 (    2)
  covalent geometry    : bond        0.00234 ( 6811)
  covalent geometry    : angle       0.45670 ( 9304)

*********************** 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: 13
    poor density    : 80
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  330 GLU cc_start: 0.7103 (tt0) cc_final: 0.6552 (tt0)
REVERT: B  175 GLN cc_start: 0.8232 (mm110) cc_final: 0.8014 (tp40)
REVERT: B  234 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8311 (m-80)
REVERT: R   65 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8216 (mt0)
  outliers start: 13
  outliers final: 5
  residues processed: 87
  average time/residue: 0.9743
  time to fit residues: 90.7474
Evaluate side-chains
  83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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  114 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   65 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 5 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0050
   chunk 83 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 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 = 0.3410 r_free = 0.3410 target = 0.125065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.101943 restraints weight = 8919.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.75
r_work: 0.2997 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6812  Z= 0.090
  Angle     :  0.435   6.186   9306  Z= 0.232
  Chirality :  0.040   0.212   1104
  Planarity :  0.003   0.031   1164
  Dihedral  :  7.478 147.384    976
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.44 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.28), residues: 873
  helix:  1.88 (0.27), residues: 394
  sheet:  0.79 (0.42), residues: 159
  loop : -0.53 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.001   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  343)
  hydrogen bonds       : angle       3.97484 (  999)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.92044 (    2)
  covalent geometry    : bond        0.00185 ( 6811)
  covalent geometry    : angle       0.43512 ( 9304)

*********************** 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
  89 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.761 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8235 (mm110) cc_final: 0.8024 (tp40)
REVERT: B  234 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8514 (m-80)
REVERT: R   65 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8176 (mt0)
  outliers start: 10
  outliers final: 5
  residues processed: 85
  average time/residue: 0.9611
  time to fit residues: 87.1712
Evaluate side-chains
  84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
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  234 PHE
Chi-restraints excluded: chain R residue   65 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0670
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** 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 = 0.3397 r_free = 0.3397 target = 0.124054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.100869 restraints weight = 8909.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.75
r_work: 0.2981 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6812  Z= 0.101
  Angle     :  0.447   6.252   9306  Z= 0.238
  Chirality :  0.040   0.130   1104
  Planarity :  0.003   0.033   1164
  Dihedral  :  7.438 147.334    976
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.37 %
    Favored  : 82.92 %
  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:  1.23 (0.28), residues: 873
  helix:  1.89 (0.27), residues: 395
  sheet:  0.83 (0.42), residues: 158
  loop : -0.52 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  343)
  hydrogen bonds       : angle       3.97108 (  999)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       1.12928 (    2)
  covalent geometry    : bond        0.00220 ( 6811)
  covalent geometry    : angle       0.44696 ( 9304)

*********************** 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
  90 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.714 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8226 (mm110) cc_final: 0.8012 (tp40)
REVERT: B  234 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8525 (m-80)
REVERT: R   65 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8205 (mt0)
  outliers start: 11
  outliers final: 6
  residues processed: 85
  average time/residue: 1.0396
  time to fit residues: 93.8902
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  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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  114 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   65 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0670
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.123235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.099993 restraints weight = 8830.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.74
r_work: 0.2981 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6812  Z= 0.102
  Angle     :  0.450   6.268   9306  Z= 0.240
  Chirality :  0.041   0.215   1104
  Planarity :  0.003   0.033   1164
  Dihedral  :  7.419 147.224    976
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.37 %
    Favored  : 83.23 %
  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 (0.28), residues: 873
  helix:  1.91 (0.27), residues: 396
  sheet:  0.89 (0.42), residues: 156
  loop : -0.55 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  343)
  hydrogen bonds       : angle       3.96553 (  999)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       1.14382 (    2)
  covalent geometry    : bond        0.00223 ( 6811)
  covalent geometry    : angle       0.44959 ( 9304)

*********************** 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
  85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.779 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8221 (mm110) cc_final: 0.8008 (tp40)
REVERT: B  234 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8604 (m-80)
REVERT: R   65 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8204 (mt0)
  outliers start: 9
  outliers final: 6
  residues processed: 81
  average time/residue: 1.0464
  time to fit residues: 90.2597
Evaluate side-chains
  84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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  114 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   65 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 81 optimal weight:    0.4980
   chunk 26 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.100817 restraints weight = 9038.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.76
r_work: 0.2967 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6812  Z= 0.101
  Angle     :  0.450   6.266   9306  Z= 0.240
  Chirality :  0.040   0.130   1104
  Planarity :  0.003   0.033   1164
  Dihedral  :  7.391 146.968    976
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.53 %
    Favored  : 82.92 %
  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:  1.25 (0.28), residues: 873
  helix:  1.92 (0.27), residues: 395
  sheet:  0.81 (0.42), residues: 158
  loop : -0.51 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.001   0.000   ARG A 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  343)
  hydrogen bonds       : angle       3.97019 (  999)
  SS BOND              : bond        0.00182 (    1)
  SS BOND              : angle       1.13175 (    2)
  covalent geometry    : bond        0.00221 ( 6811)
  covalent geometry    : angle       0.44990 ( 9304)

********************** 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
  84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.782 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8192 (mm110) cc_final: 0.7973 (tp40)
REVERT: B  234 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8587 (m-80)
REVERT: R   65 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8210 (mt0)
  outliers start: 10
  outliers final: 6
  residues processed: 80
  average time/residue: 0.9988
  time to fit residues: 85.2114
Evaluate side-chains
  81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
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  114 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   65 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0370
   chunk 62 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0030
   chunk 81 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4668

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.124846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.101848 restraints weight = 8856.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 1.71
r_work: 0.3007 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6812  Z= 0.088
  Angle     :  0.431   6.218   9306  Z= 0.230
  Chirality :  0.040   0.225   1104
  Planarity :  0.003   0.030   1164
  Dihedral  :  7.296 146.073    976
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.68 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.32 (0.29), residues: 873
  helix:  2.02 (0.27), residues: 395
  sheet:  0.82 (0.42), residues: 158
  loop : -0.52 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 292 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.001   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  343)
  hydrogen bonds       : angle       3.90525 (  999)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.88200 (    2)
  covalent geometry    : bond        0.00179 ( 6811)
  covalent geometry    : angle       0.43043 ( 9304)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5022.07 seconds
wall clock time: 88 minutes 14.21 seconds (5294.21 seconds total)