Starting phenix.real_space_refine
on Tue Feb 11 22:39:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gge_40004/02_2025/8gge_40004.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gge_40004/02_2025/8gge_40004.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gge_40004/02_2025/8gge_40004.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gge_40004/02_2025/8gge_40004.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gge_40004/02_2025/8gge_40004.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gge_40004/02_2025/8gge_40004.cif"
  }
  resolution = 3.5
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      32      5.16       5
     C    4236      2.51       5
     N    1204      2.21       5
     O    1233      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6708
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2526
          Classifications: {'peptide': 361}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 133}
          Link IDs: {'PTRANS': 13, 'TRANS': 347}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 476
          Unresolved non-hydrogen angles: 592
          Unresolved non-hydrogen dihedrals: 378
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 304
    Chain: "B"
      Number of atoms: 2408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2408
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 143
    Chain: "G"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 340
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "R"
      Number of atoms: 1387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1387
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 142}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 7
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 505
          Unresolved non-hydrogen angles: 664
          Unresolved non-hydrogen dihedrals: 417
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 9, 'GLU:plan': 6, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 252
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.71, per 1000 atoms: 0.70
  Number of scatterers: 6708
  At special positions: 0
  Unit cell: (84.1669, 136.229, 103.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       3     15.00
     O    1233      8.00
     N    1204      7.00
     C    4236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.88
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1870

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      47.1% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.938A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.704A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 113
      removed outlier: 3.600A  pdb=" N   GLU A 104 " --> pdb=" O   LYS A 100 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   SER A 111 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 4.135A  pdb=" N   TYR A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 4.021A  pdb=" N   TYR A 147 " --> pdb=" O   PRO A 143 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU A 148 " --> pdb=" O   PRO A 144 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   HIS A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 164
    Processing helix  chain 'A' and resid 175 through 181
      removed outlier: 3.673A  pdb=" N   LYS A 181 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.995A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 4.069A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.009A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.610A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 389
      removed outlier: 3.843A  pdb=" N   ILE A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   GLN A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 4.054A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.826A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.731A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.756A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.659A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 54
      removed outlier: 4.223A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU R  45 " --> pdb=" O   SER R  41 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 70 through 78
      removed outlier: 4.259A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU R  75 " --> pdb=" O   PHE R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 94
      removed outlier: 4.065A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.706A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP R 113 " --> pdb=" O   TRP R 109 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 171
      removed outlier: 3.633A  pdb=" N   MET R 156 " --> pdb=" O   VAL R 152 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.870A  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 198 through 208
    Processing helix  chain 'R' and resid 208 through 230
      removed outlier: 4.170A  pdb=" N   LEU R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL R 216 " --> pdb=" O   LEU R 212 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   PHE R 217 " --> pdb=" O   VAL R 213 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   TYR R 219 " --> pdb=" O   MET R 215 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL R 222 " --> pdb=" O   VAL R 218 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS R 227 " --> pdb=" O   PHE R 223 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG R 228 " --> pdb=" O   GLN R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 287
      removed outlier: 3.641A  pdb=" N   GLY R 276 " --> pdb=" O   LEU R 272 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ILE R 277 " --> pdb=" O   LYS R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 299
      removed outlier: 3.733A  pdb=" N   ILE R 291 " --> pdb=" O   LEU R 287 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL R 295 " --> pdb=" O   ILE R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 314
    Processing helix  chain 'R' and resid 317 through 326
      Proline residue:  R 323  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 3.952A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 9.475A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.674A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.937A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.856A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B  81 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.508A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.902A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.723A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.595A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.756A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    909 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: 2.04

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1797
        1.33 -     1.45: 1256
        1.45 -     1.57: 3726
        1.57 -     1.69: 6
        1.69 -     1.81: 44
  Bond restraints: 6829
  Sorted by residual:
  bond pdb=" CA  GLN A 384 "
       pdb=" C   GLN A 384 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.082 1.32e-02 5.74e+03 3.86e+01
  bond pdb=" N   ARG A 385 "
       pdb=" CA  ARG A 385 "
    ideal  model  delta    sigma   weight residual
    1.459  1.408  0.051 1.19e-02 7.06e+03 1.85e+01
  bond pdb=" CA  PHE A 376 "
       pdb=" C   PHE A 376 "
    ideal  model  delta    sigma   weight residual
    1.526  1.474  0.052 1.39e-02 5.18e+03 1.40e+01
  bond pdb=" CA  LEU A 388 "
       pdb=" C   LEU A 388 "
    ideal  model  delta    sigma   weight residual
    1.523  1.475  0.048 1.30e-02 5.92e+03 1.38e+01
  bond pdb=" CA  ASP A 381 "
       pdb=" C   ASP A 381 "
    ideal  model  delta    sigma   weight residual
    1.527  1.481  0.046 1.30e-02 5.92e+03 1.26e+01
  ... (remaining 6824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 9247
        2.17 -     4.35: 84
        4.35 -     6.52: 18
        6.52 -     8.69: 4
        8.69 -    10.87: 4
  Bond angle restraints: 9357
  Sorted by residual:
  angle pdb=" N   HIS A 387 "
        pdb=" CA  HIS A 387 "
        pdb=" C   HIS A 387 "
      ideal   model   delta    sigma   weight residual
     111.14  121.58  -10.44 1.08e+00 8.57e-01 9.34e+01
  angle pdb=" N   TYR A 391 "
        pdb=" CA  TYR A 391 "
        pdb=" C   TYR A 391 "
      ideal   model   delta    sigma   weight residual
     113.43  102.56   10.87 1.26e+00 6.30e-01 7.44e+01
  angle pdb=" N   ASP A 381 "
        pdb=" CA  ASP A 381 "
        pdb=" C   ASP A 381 "
      ideal   model   delta    sigma   weight residual
     111.39  102.62    8.77 1.38e+00 5.25e-01 4.04e+01
  angle pdb=" N   PHE A 376 "
        pdb=" CA  PHE A 376 "
        pdb=" C   PHE A 376 "
      ideal   model   delta    sigma   weight residual
     111.90  103.54    8.36 1.32e+00 5.74e-01 4.01e+01
  angle pdb=" N   CYS A 379 "
        pdb=" CA  CYS A 379 "
        pdb=" C   CYS A 379 "
      ideal   model   delta    sigma   weight residual
     111.52  102.69    8.83 1.40e+00 5.10e-01 3.98e+01
  ... (remaining 9352 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 3667
       17.57 -    35.15: 239
       35.15 -    52.72: 41
       52.72 -    70.29: 4
       70.29 -    87.86: 3
  Dihedral angle restraints: 3954
    sinusoidal: 1088
      harmonic: 2866
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   18.88   85.71     1      2.00e+01 2.50e-03 2.22e+01
  dihedral pdb=" CA  GLU A 259 "
           pdb=" C   GLU A 259 "
           pdb=" N   ASP A 260 "
           pdb=" CA  ASP A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.32  -19.68     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CB  LYS B  89 "
           pdb=" CG  LYS B  89 "
           pdb=" CD  LYS B  89 "
           pdb=" CE  LYS B  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.82   49.82     3      1.50e+01 4.44e-03 8.82e+00
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 916
       0.051 -    0.103: 176
       0.103 -    0.154: 34
       0.154 -    0.205: 2
       0.205 -    0.257: 1
  Chirality restraints: 1129
  Sorted by residual:
  chirality pdb=" CA  HIS A 387 "
            pdb=" N   HIS A 387 "
            pdb=" C   HIS A 387 "
            pdb=" CB  HIS A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  GLU A 392 "
            pdb=" N   GLU A 392 "
            pdb=" C   GLU A 392 "
            pdb=" CB  GLU A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.20e-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    2.56   -0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 1126 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 375 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   VAL A 375 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A 375 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 376 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 393 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" C   LEU A 393 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU A 393 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A 394 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO G  49 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1249
        2.77 -     3.30: 6258
        3.30 -     3.83: 10166
        3.83 -     4.37: 10536
        4.37 -     4.90: 19574
  Nonbonded interactions: 47783
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NZ  LYS A  53 "
            pdb=" O1G GTP A 401 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   VAL A 375 "
            pdb=" N   ASP A 378 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   MET R 171 "
            pdb=" ND1 HIS R 172 "
     model   vdw
     2.287 3.120
  ... (remaining 47778 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.290
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.870
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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   0.082   6829  Z= 0.231
  Angle     :  0.593  10.867   9357  Z= 0.358
  Chirality :  0.042   0.257   1129
  Planarity :  0.003   0.041   1203
  Dihedral  : 12.439  87.864   2084
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -0.02 (0.28), residues: 954
  helix:  1.70 (0.28), residues: 377
  sheet: -1.02 (0.40), residues: 184
  loop : -1.17 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 286 
 HIS   0.006   0.001   HIS A 387 
 PHE   0.021   0.001   PHE R 289 
 TYR   0.009   0.001   TYR R 174 
 ARG   0.007   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  331 ASP cc_start: 0.8236 (t0) cc_final: 0.7971 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1501
  time to fit residues: 19.6775
Evaluate side-chains
  73 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    0.4980
   chunk 76 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 384 GLN
B  88 ASN
B 295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.137411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.101024 restraints weight = 11925.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103721 restraints weight = 6746.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105555 restraints weight = 4847.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6829  Z= 0.327
  Angle     :  0.559   6.033   9357  Z= 0.307
  Chirality :  0.044   0.151   1129
  Planarity :  0.004   0.050   1203
  Dihedral  :  5.394  87.099   1059
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.77 %
    Favored  : 85.66 %
  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: -0.10 (0.28), residues: 954
  helix:  1.58 (0.27), residues: 400
  sheet: -1.06 (0.40), residues: 181
  loop : -1.35 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R  99 
 HIS   0.007   0.002   HIS A 387 
 PHE   0.029   0.002   PHE B 234 
 TYR   0.019   0.002   TYR R 174 
 ARG   0.004   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.8080 (t-100) cc_final: 0.7266 (t-100)
REVERT: A  331 ASP cc_start: 0.7614 (t0) cc_final: 0.7367 (t70)
  outliers start: 8
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1334
  time to fit residues: 16.5418
Evaluate side-chains
  77 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  158 TRP
Chi-restraints excluded: chain R residue  174 TYR
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0770
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.103532 restraints weight = 11959.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.106438 restraints weight = 6722.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.108350 restraints weight = 4788.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6829  Z= 0.148
  Angle     :  0.461   6.155   9357  Z= 0.251
  Chirality :  0.042   0.154   1129
  Planarity :  0.003   0.044   1203
  Dihedral  :  5.038  85.019   1059
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 17.29 %
    Favored  : 81.53 %
  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:  0.14 (0.28), residues: 954
  helix:  1.73 (0.27), residues: 411
  sheet: -0.77 (0.40), residues: 183
  loop : -1.35 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R  99 
 HIS   0.008   0.001   HIS A 387 
 PHE   0.022   0.001   PHE R 282 
 TYR   0.011   0.001   TYR R 174 
 ARG   0.005   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.8047 (t-100) cc_final: 0.7257 (t-100)
REVERT: A  211 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8719 (mmtm)
REVERT: A  331 ASP cc_start: 0.7449 (t0) cc_final: 0.7092 (t70)
REVERT: A  368 ASP cc_start: 0.7935 (t0) cc_final: 0.7686 (t0)
REVERT: B   58 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8039 (mp)
  outliers start: 6
  outliers final: 2
  residues processed: 84
  average time/residue: 0.1451
  time to fit residues: 18.4381
Evaluate side-chains
  75 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 69 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.140048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.103723 restraints weight = 12030.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.106501 restraints weight = 6667.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.108375 restraints weight = 4757.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6829  Z= 0.155
  Angle     :  0.453   6.222   9357  Z= 0.247
  Chirality :  0.042   0.158   1129
  Planarity :  0.003   0.044   1203
  Dihedral  :  4.912  84.317   1059
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.68 %
    Favored  : 80.35 %
  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:  0.32 (0.28), residues: 954
  helix:  1.92 (0.27), residues: 411
  sheet: -0.62 (0.40), residues: 179
  loop : -1.35 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R  99 
 HIS   0.007   0.001   HIS A 387 
 PHE   0.025   0.001   PHE R 282 
 TYR   0.010   0.001   TYR A 130 
 ARG   0.005   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.8013 (t-100) cc_final: 0.7197 (t-100)
REVERT: A  209 GLU cc_start: 0.8254 (tt0) cc_final: 0.8026 (tt0)
REVERT: A  331 ASP cc_start: 0.7360 (t0) cc_final: 0.6913 (t70)
REVERT: A  368 ASP cc_start: 0.7947 (t0) cc_final: 0.7574 (t0)
REVERT: B  262 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7993 (mpp)
REVERT: R  215 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6331 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1280
  time to fit residues: 15.4850
Evaluate side-chains
  76 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.140577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.104068 restraints weight = 11885.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.106983 restraints weight = 6564.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.108938 restraints weight = 4632.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   6829  Z= 0.140
  Angle     :  0.442   6.231   9357  Z= 0.241
  Chirality :  0.041   0.141   1129
  Planarity :  0.003   0.042   1203
  Dihedral  :  4.837  83.684   1059
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.25 %
    Favored  : 78.78 %
  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:  0.38 (0.28), residues: 954
  helix:  2.01 (0.27), residues: 411
  sheet: -0.55 (0.40), residues: 181
  loop : -1.41 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  99 
 HIS   0.007   0.001   HIS A 387 
 PHE   0.025   0.001   PHE R 282 
 TYR   0.013   0.001   TYR R 308 
 ARG   0.005   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7976 (t-100) cc_final: 0.7145 (t-100)
REVERT: A  211 LYS cc_start: 0.9017 (mptt) cc_final: 0.8767 (mmtt)
REVERT: A  331 ASP cc_start: 0.7345 (t0) cc_final: 0.6934 (t70)
REVERT: B  262 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7869 (mpp)
REVERT: R  215 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6325 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1221
  time to fit residues: 15.6733
Evaluate side-chains
  81 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0050
   chunk 82 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 84 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 56 optimal weight:    0.7980
   chunk 72 optimal weight:    7.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.141016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.104427 restraints weight = 11873.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.107309 restraints weight = 6531.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.109122 restraints weight = 4625.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6829  Z= 0.128
  Angle     :  0.442   6.236   9357  Z= 0.240
  Chirality :  0.041   0.153   1129
  Planarity :  0.003   0.043   1203
  Dihedral  :  4.768  83.140   1059
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.04 %
    Favored  : 78.19 %
  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:  0.47 (0.28), residues: 954
  helix:  2.07 (0.27), residues: 411
  sheet: -0.43 (0.41), residues: 174
  loop : -1.37 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R  99 
 HIS   0.006   0.001   HIS R 172 
 PHE   0.025   0.001   PHE R 282 
 TYR   0.009   0.001   TYR A 130 
 ARG   0.004   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7902 (t-100) cc_final: 0.7081 (t-100)
REVERT: A  211 LYS cc_start: 0.8923 (mptt) cc_final: 0.8687 (mmtm)
REVERT: A  331 ASP cc_start: 0.7288 (t0) cc_final: 0.6888 (t70)
REVERT: R  215 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6264 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 81
  average time/residue: 0.1327
  time to fit residues: 16.2590
Evaluate side-chains
  79 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0970
   chunk 40 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0970
   chunk 10 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0980
   chunk 62 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0980
   chunk 55 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.143372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.106874 restraints weight = 11772.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.109715 restraints weight = 6553.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.111703 restraints weight = 4653.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.017   6829  Z= 0.100
  Angle     :  0.422   6.271   9357  Z= 0.227
  Chirality :  0.040   0.140   1129
  Planarity :  0.003   0.040   1203
  Dihedral  :  4.527  80.587   1059
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 20.43 %
    Favored  : 78.19 %
  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:  0.69 (0.28), residues: 954
  helix:  2.24 (0.27), residues: 409
  sheet: -0.24 (0.42), residues: 173
  loop : -1.27 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.006   0.001   HIS R 172 
 PHE   0.027   0.001   PHE R 282 
 TYR   0.011   0.001   TYR A 130 
 ARG   0.004   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  154 TRP cc_start: 0.7869 (t-100) cc_final: 0.6984 (t-100)
REVERT: A  211 LYS cc_start: 0.8905 (mptt) cc_final: 0.8679 (mmtm)
REVERT: A  331 ASP cc_start: 0.7153 (t0) cc_final: 0.6757 (t70)
REVERT: A  352 SER cc_start: 0.7303 (m) cc_final: 0.7022 (t)
REVERT: R  215 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6199 (mmm)
  outliers start: 7
  outliers final: 4
  residues processed: 85
  average time/residue: 0.1247
  time to fit residues: 15.9939
Evaluate side-chains
  78 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 96 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.141698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.105305 restraints weight = 11992.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.108206 restraints weight = 6518.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.110040 restraints weight = 4593.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6829  Z= 0.134
  Angle     :  0.443   6.660   9357  Z= 0.237
  Chirality :  0.041   0.154   1129
  Planarity :  0.003   0.040   1203
  Dihedral  :  4.593  80.913   1059
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.04 %
    Favored  : 77.80 %
  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:  0.77 (0.29), residues: 954
  helix:  2.32 (0.27), residues: 408
  sheet: -0.25 (0.42), residues: 173
  loop : -1.20 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.006   0.001   HIS R 172 
 PHE   0.026   0.001   PHE R 282 
 TYR   0.015   0.001   TYR R 308 
 ARG   0.003   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  331 ASP cc_start: 0.7211 (t0) cc_final: 0.6816 (t70)
REVERT: A  352 SER cc_start: 0.7366 (m) cc_final: 0.7040 (t)
REVERT: R  215 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6008 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1337
  time to fit residues: 16.3403
Evaluate side-chains
  80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 78 optimal weight:   20.0000
   chunk 19 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.3198

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.139310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103046 restraints weight = 12125.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.105867 restraints weight = 6673.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.107568 restraints weight = 4751.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6829  Z= 0.219
  Angle     :  0.480   7.791   9357  Z= 0.258
  Chirality :  0.042   0.143   1129
  Planarity :  0.003   0.041   1203
  Dihedral  :  4.874  82.860   1059
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.24 %
    Favored  : 77.60 %
  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:  0.61 (0.29), residues: 954
  helix:  2.23 (0.27), residues: 410
  sheet: -0.44 (0.42), residues: 176
  loop : -1.30 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 
 PHE   0.027   0.002   PHE R 282 
 TYR   0.009   0.001   TYR A 391 
 ARG   0.006   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  331 ASP cc_start: 0.7353 (t0) cc_final: 0.7029 (t70)
REVERT: B  292 PHE cc_start: 0.8904 (m-80) cc_final: 0.8415 (m-80)
REVERT: R  215 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6031 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1457
  time to fit residues: 17.6660
Evaluate side-chains
  79 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 94 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 78 optimal weight:   20.0000
   chunk 19 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.136580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100458 restraints weight = 12200.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.103105 restraints weight = 6747.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.105002 restraints weight = 4832.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6829  Z= 0.339
  Angle     :  0.569   8.134   9357  Z= 0.303
  Chirality :  0.044   0.153   1129
  Planarity :  0.004   0.043   1203
  Dihedral  :  5.322  84.856   1059
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.83 %
    Favored  : 77.41 %
  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:  0.29 (0.29), residues: 954
  helix:  1.92 (0.27), residues: 410
  sheet: -0.58 (0.42), residues: 176
  loop : -1.43 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.007   0.002   HIS R 172 
 PHE   0.028   0.002   PHE R 282 
 TYR   0.019   0.002   TYR A 391 
 ARG   0.007   0.000   ARG G  27 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  331 ASP cc_start: 0.7613 (t0) cc_final: 0.7246 (t70)
REVERT: A  368 ASP cc_start: 0.8135 (t70) cc_final: 0.7644 (t0)
REVERT: R  215 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6195 (mtm)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1348
  time to fit residues: 15.7277
Evaluate side-chains
  77 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  376 PHE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain R residue  215 MET
Chi-restraints excluded: chain R residue  218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.138962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.102609 restraints weight = 12054.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.105407 restraints weight = 6672.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.107260 restraints weight = 4750.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6829  Z= 0.170
  Angle     :  0.490   7.806   9357  Z= 0.261
  Chirality :  0.042   0.142   1129
  Planarity :  0.003   0.040   1203
  Dihedral  :  5.116  84.388   1059
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.02 %
    Favored  : 77.21 %
  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:  0.41 (0.29), residues: 954
  helix:  2.07 (0.27), residues: 410
  sheet: -0.52 (0.42), residues: 176
  loop : -1.43 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 172 
 PHE   0.026   0.001   PHE R 282 
 TYR   0.021   0.001   TYR A 391 
 ARG   0.007   0.000   ARG G  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2395.33 seconds
wall clock time: 43 minutes 21.63 seconds (2601.63 seconds total)