Starting phenix.real_space_refine
on Mon Apr 28 01:54:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gg5_29995/04_2025/8gg5_29995.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gg5_29995/04_2025/8gg5_29995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gg5_29995/04_2025/8gg5_29995.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gg5_29995/04_2025/8gg5_29995.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gg5_29995/04_2025/8gg5_29995.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gg5_29995/04_2025/8gg5_29995.cif"
  }
  resolution = 3.2
  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=   0.027
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      47      5.16       5
     C    4351      2.51       5
     N    1167      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 3 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: 6799
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1799
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 122
    Chain: "B"
      Number of atoms: 2456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2456
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 100
    Chain: "G"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 335
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          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: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 2157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2157
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 70
    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: 5.08, per 1000 atoms: 0.75
  Number of scatterers: 6799
  At special positions: 0
  Unit cell: (85.0346, 133.626, 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      47     16.00
     P       3     15.00
     O    1231      8.00
     N    1167      7.00
     C    4351      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 1.50
  Conformation dependent library (CDL) restraints added in 896.1 milliseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1710

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      48.9% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.820A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.532A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 4.007A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.615A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.699A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.258A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.556A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.753A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 25
      removed outlier: 3.596A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.978A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.750A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 34 through 61
      removed outlier: 3.702A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER R  41 " --> pdb=" O   GLY R  37 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU R  42 " --> pdb=" O   ILE R  38 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 67 through 86
      removed outlier: 4.319A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 103 through 137
      removed outlier: 4.193A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.016A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.549A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.676A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 268 through 299
      removed outlier: 3.677A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.441A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.622A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 322
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.967A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.713A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.646A  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: 3.892A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.592A  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: 7.111A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.055A  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 153
      removed outlier: 6.827A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.335A  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: 6.838A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.610A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.778A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    993 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: 1.81

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2185
        1.34 -     1.46: 1621
        1.46 -     1.58: 3065
        1.58 -     1.70: 5
        1.70 -     1.81: 66
  Bond restraints: 6942
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.52e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.93e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.435 -0.041 2.00e-02 2.50e+03 4.13e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.563 -0.040 2.00e-02 2.50e+03 3.90e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.318  0.035 2.00e-02 2.50e+03 3.14e+00
  ... (remaining 6937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 9312
        1.51 -     3.02: 129
        3.02 -     4.53: 25
        4.53 -     6.04: 7
        6.04 -     7.55: 2
  Bond angle restraints: 9475
  Sorted by residual:
  angle pdb=" C2' GTP A 401 "
        pdb=" C3' GTP A 401 "
        pdb=" C4' GTP A 401 "
      ideal   model   delta    sigma   weight residual
     111.00  103.45    7.55 3.00e+00 1.11e-01 6.33e+00
  angle pdb=" N   PHE B 234 "
        pdb=" CA  PHE B 234 "
        pdb=" C   PHE B 234 "
      ideal   model   delta    sigma   weight residual
     110.50  113.78   -3.28 1.41e+00 5.03e-01 5.42e+00
  angle pdb=" N   LEU R 287 "
        pdb=" CA  LEU R 287 "
        pdb=" C   LEU R 287 "
      ideal   model   delta    sigma   weight residual
     109.81  114.33   -4.52 2.21e+00 2.05e-01 4.19e+00
  angle pdb=" C   GLU A 330 "
        pdb=" CA  GLU A 330 "
        pdb=" CB  GLU A 330 "
      ideal   model   delta    sigma   weight residual
     110.36  113.80   -3.44 1.78e+00 3.16e-01 3.74e+00
  angle pdb=" CA  LEU B 318 "
        pdb=" CB  LEU B 318 "
        pdb=" CG  LEU B 318 "
      ideal   model   delta    sigma   weight residual
     116.30  122.96   -6.66 3.50e+00 8.16e-02 3.62e+00
  ... (remaining 9470 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.79: 3976
       34.79 -    69.58: 62
       69.58 -   104.37: 5
      104.37 -   139.16: 0
      139.16 -   173.95: 1
  Dihedral angle restraints: 4044
    sinusoidal: 1409
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" C4' GTP A 401 "
           pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87   86.93  173.95     1      2.00e+01 2.50e-03 4.79e+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   11.47   93.12     1      2.00e+01 2.50e-03 2.53e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.74   18.26     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 4041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 601
       0.026 -    0.052: 290
       0.052 -    0.078: 145
       0.078 -    0.104: 51
       0.104 -    0.130: 32
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.53   -0.13 2.00e-01 2.50e+01 4.20e-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 4.01e-01
  ... (remaining 1116 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "   -0.027 5.00e-02 4.00e+02   4.08e-02 2.67e+00
        pdb=" N   PRO B  39 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO A 332 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO B 236 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1966
        2.81 -     3.34: 5969
        3.34 -     3.86: 10378
        3.86 -     4.38: 11880
        4.38 -     4.90: 21982
  Nonbonded interactions: 52175
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD2 ASP B  76 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" NE2 GLN G  18 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   TYR A 253 "
            pdb=" ND2 ASN A 264 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" OD2 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.336 3.040
  ... (remaining 52170 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.080
  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:                    0.060
  Process input model:                     19.230
  Find NCS groups from input model:        0.060
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
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      :  0.004   0.051   6944  Z= 0.171
  Angle     :  0.516   7.549   9479  Z= 0.272
  Chirality :  0.042   0.130   1119
  Planarity :  0.004   0.041   1186
  Dihedral  : 14.022 173.947   2328
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.28), residues: 890
  helix:  1.46 (0.27), residues: 385
  sheet: -0.52 (0.39), residues: 166
  loop : -0.71 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  63 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.014   0.002   PHE R  49 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22840 (  342)
  hydrogen bonds       : angle       6.22226 (  993)
  SS BOND              : bond        0.00165 (    2)
  SS BOND              : angle       0.53037 (    4)
  covalent geometry    : bond        0.00395 ( 6942)
  covalent geometry    : angle       0.51608 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8339 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2035
  time to fit residues: 23.3640
Evaluate side-chains
  73 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 37 optimal weight:    0.1980
   chunk 23 optimal weight:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.143535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.113429 restraints weight = 8656.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.13
r_work: 0.2993 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6944  Z= 0.118
  Angle     :  0.482   7.374   9479  Z= 0.261
  Chirality :  0.041   0.131   1119
  Planarity :  0.003   0.035   1186
  Dihedral  :  7.417 173.463    993
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.61 %
    Favored  : 92.79 %
  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: 890
  helix:  1.69 (0.27), residues: 397
  sheet:  0.03 (0.42), residues: 159
  loop : -0.73 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 277 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.006   0.001   TYR B 105 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05400 (  342)
  hydrogen bonds       : angle       4.30111 (  993)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.72205 (    4)
  covalent geometry    : bond        0.00235 ( 6942)
  covalent geometry    : angle       0.48233 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.695 
Fit side-chains
REVERT: R  156 MET cc_start: 0.8321 (mtp) cc_final: 0.8095 (mtp)
  outliers start: 4
  outliers final: 3
  residues processed: 85
  average time/residue: 0.1887
  time to fit residues: 22.0962
Evaluate side-chains
  78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain R residue   94 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 66 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** 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 = 0.3687 r_free = 0.3687 target = 0.144681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114632 restraints weight = 8677.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.10
r_work: 0.2975 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6944  Z= 0.120
  Angle     :  0.470   7.480   9479  Z= 0.251
  Chirality :  0.041   0.137   1119
  Planarity :  0.003   0.032   1186
  Dihedral  :  7.400 174.778    993
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.46 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 890
  helix:  1.84 (0.26), residues: 397
  sheet:  0.18 (0.42), residues: 159
  loop : -0.76 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.011   0.001   PHE R  49 
 TYR   0.007   0.001   TYR B 105 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05223 (  342)
  hydrogen bonds       : angle       4.02813 (  993)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.64629 (    4)
  covalent geometry    : bond        0.00261 ( 6942)
  covalent geometry    : angle       0.46957 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.752 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1753
  time to fit residues: 19.4473
Evaluate side-chains
  76 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 79 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0770
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** 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 = 0.3636 r_free = 0.3636 target = 0.141403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.110462 restraints weight = 8852.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.18
r_work: 0.2990 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6944  Z= 0.110
  Angle     :  0.459   7.402   9479  Z= 0.245
  Chirality :  0.040   0.134   1119
  Planarity :  0.003   0.033   1186
  Dihedral  :  7.339 174.042    993
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 12.61 %
    Favored  : 86.49 %
  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:  0.99 (0.28), residues: 890
  helix:  1.97 (0.26), residues: 398
  sheet:  0.26 (0.43), residues: 159
  loop : -0.76 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.006   0.001   TYR B 105 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04714 (  342)
  hydrogen bonds       : angle       3.91435 (  993)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.64350 (    4)
  covalent geometry    : bond        0.00237 ( 6942)
  covalent geometry    : angle       0.45866 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.705 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 82
  average time/residue: 0.1972
  time to fit residues: 21.6979
Evaluate side-chains
  77 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  322 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 15 optimal weight:    0.0060
   chunk 57 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0370
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5074

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** 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 = 0.3679 r_free = 0.3679 target = 0.144373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113876 restraints weight = 8690.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.14
r_work: 0.3010 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6944  Z= 0.098
  Angle     :  0.438   7.303   9479  Z= 0.234
  Chirality :  0.040   0.132   1119
  Planarity :  0.003   0.033   1186
  Dihedral  :  7.270 173.256    993
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.21 %
    Favored  : 86.04 %
  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:  1.16 (0.28), residues: 890
  helix:  2.11 (0.26), residues: 400
  sheet:  0.34 (0.43), residues: 160
  loop : -0.67 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 277 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  342)
  hydrogen bonds       : angle       3.79864 (  993)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.61061 (    4)
  covalent geometry    : bond        0.00202 ( 6942)
  covalent geometry    : angle       0.43750 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8336 (m-30) cc_final: 0.7929 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1830
  time to fit residues: 20.3967
Evaluate side-chains
  78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain R residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0670
   chunk 73 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.140632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.110180 restraints weight = 8728.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.12
r_work: 0.2928 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6944  Z= 0.202
  Angle     :  0.545   7.813   9479  Z= 0.290
  Chirality :  0.044   0.143   1119
  Planarity :  0.004   0.034   1186
  Dihedral  :  7.569 176.245    993
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 15.17 %
    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:  0.85 (0.28), residues: 890
  helix:  1.83 (0.26), residues: 397
  sheet:  0.09 (0.41), residues: 166
  loop : -0.72 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.014   0.002   PHE R 282 
 TYR   0.010   0.001   TYR B 105 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06193 (  342)
  hydrogen bonds       : angle       4.16233 (  993)
  SS BOND              : bond        0.00234 (    2)
  SS BOND              : angle       0.57593 (    4)
  covalent geometry    : bond        0.00490 ( 6942)
  covalent geometry    : angle       0.54468 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.797 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 77
  average time/residue: 0.1931
  time to fit residues: 20.2486
Evaluate side-chains
  77 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0670
   chunk 53 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0970
   chunk 7 optimal weight:    0.0370
   overall best weight:    0.3394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.117065 restraints weight = 8608.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.09
r_work: 0.3043 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6944  Z= 0.090
  Angle     :  0.437   7.254   9479  Z= 0.234
  Chirality :  0.040   0.131   1119
  Planarity :  0.003   0.033   1186
  Dihedral  :  7.275 172.976    993
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 15.47 %
    Favored  : 83.63 %
  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:  1.17 (0.28), residues: 890
  helix:  2.11 (0.26), residues: 400
  sheet:  0.29 (0.43), residues: 165
  loop : -0.64 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 277 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  342)
  hydrogen bonds       : angle       3.81384 (  993)
  SS BOND              : bond        0.00186 (    2)
  SS BOND              : angle       0.69564 (    4)
  covalent geometry    : bond        0.00174 ( 6942)
  covalent geometry    : angle       0.43721 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.808 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.2264
  time to fit residues: 24.1350
Evaluate side-chains
  76 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  137 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0050
   chunk 65 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0060
   chunk 45 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.2210

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.120303 restraints weight = 8620.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.09
r_work: 0.3117 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6944  Z= 0.082
  Angle     :  0.415   7.061   9479  Z= 0.221
  Chirality :  0.039   0.127   1119
  Planarity :  0.003   0.033   1186
  Dihedral  :  7.083 170.510    993
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.02 %
    Favored  : 84.23 %
  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:  1.44 (0.29), residues: 890
  helix:  2.42 (0.26), residues: 398
  sheet:  0.49 (0.43), residues: 164
  loop : -0.64 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 277 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.015   0.001   PHE R  49 
 TYR   0.005   0.001   TYR R 219 
 ARG   0.003   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  342)
  hydrogen bonds       : angle       3.58853 (  993)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       0.59072 (    4)
  covalent geometry    : bond        0.00161 ( 6942)
  covalent geometry    : angle       0.41515 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.8293 (m-30) cc_final: 0.7887 (m-30)
REVERT: A  368 ASP cc_start: 0.6867 (p0) cc_final: 0.6641 (p0)
REVERT: R   51 ASN cc_start: 0.7727 (m-40) cc_final: 0.7263 (m110)
  outliers start: 5
  outliers final: 4
  residues processed: 85
  average time/residue: 0.1708
  time to fit residues: 20.2128
Evaluate side-chains
  81 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  137 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.141620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.110781 restraints weight = 8778.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 2.15
r_work: 0.2965 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6944  Z= 0.152
  Angle     :  0.502   7.819   9479  Z= 0.264
  Chirality :  0.042   0.137   1119
  Planarity :  0.003   0.032   1186
  Dihedral  :  7.325 173.760    993
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.32 %
    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:  1.29 (0.28), residues: 890
  helix:  2.30 (0.26), residues: 399
  sheet:  0.24 (0.41), residues: 166
  loop : -0.63 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.012   0.001   PHE R 282 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05064 (  342)
  hydrogen bonds       : angle       3.86728 (  993)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.51328 (    4)
  covalent geometry    : bond        0.00364 ( 6942)
  covalent geometry    : angle       0.50202 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.7084 (p0) cc_final: 0.6876 (p0)
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2641
  time to fit residues: 27.3444
Evaluate side-chains
  73 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  137 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 85 optimal weight:    0.3980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.145208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.114726 restraints weight = 8803.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.12
r_work: 0.2993 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6944  Z= 0.111
  Angle     :  0.463   7.358   9479  Z= 0.245
  Chirality :  0.041   0.135   1119
  Planarity :  0.003   0.033   1186
  Dihedral  :  7.277 173.309    993
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.47 %
    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:  1.34 (0.28), residues: 890
  helix:  2.33 (0.26), residues: 400
  sheet:  0.28 (0.41), residues: 170
  loop : -0.62 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.009   0.001   PHE R 282 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  342)
  hydrogen bonds       : angle       3.80577 (  993)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.65764 (    4)
  covalent geometry    : bond        0.00244 ( 6942)
  covalent geometry    : angle       0.46247 ( 9475)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.7083 (p0) cc_final: 0.6882 (p0)
  outliers start: 5
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1894
  time to fit residues: 19.1552
Evaluate side-chains
  74 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0980
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0770
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.146067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.115781 restraints weight = 8683.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.10
r_work: 0.3009 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6944  Z= 0.105
  Angle     :  0.454   7.277   9479  Z= 0.240
  Chirality :  0.040   0.141   1119
  Planarity :  0.003   0.033   1186
  Dihedral  :  7.237 172.678    993
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.62 %
    Favored  : 83.63 %
  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:  1.39 (0.28), residues: 890
  helix:  2.39 (0.26), residues: 400
  sheet:  0.32 (0.42), residues: 165
  loop : -0.63 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 277 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.014   0.001   PHE R  49 
 TYR   0.006   0.001   TYR R 308 
 ARG   0.004   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04286 (  342)
  hydrogen bonds       : angle       3.75376 (  993)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.63742 (    4)
  covalent geometry    : bond        0.00227 ( 6942)
  covalent geometry    : angle       0.45396 ( 9475)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4445.22 seconds
wall clock time: 78 minutes 11.13 seconds (4691.13 seconds total)