Starting phenix.real_space_refine
on Wed Jun 11 00:35:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rxk_19577/06_2025/8rxk_19577.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rxk_19577/06_2025/8rxk_19577.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rxk_19577/06_2025/8rxk_19577.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rxk_19577/06_2025/8rxk_19577.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rxk_19577/06_2025/8rxk_19577.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rxk_19577/06_2025/8rxk_19577.cif"
  }
  resolution = 3.23
  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=   0.007
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      57      5.49       5
     S      63      5.16       5
     C    7497      2.51       5
     N    2171      2.21       5
     O    2374      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12162
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 3727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 486, 3727
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 29, 'TRANS': 456}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3679
          Classifications: {'peptide': 480}
          Link IDs: {'PTRANS': 29, 'TRANS': 450}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 3679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3679
          Classifications: {'peptide': 480}
          Link IDs: {'PTRANS': 29, 'TRANS': 450}
          Chain breaks: 2
    Chain: "Y"
      Number of atoms: 480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 480
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "Z"
      Number of atoms: 504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 504
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "C"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 62
          Unusual residues: {'ANP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.09, per 1000 atoms: 0.75
  Number of scatterers: 12162
  At special positions: 0
  Unit cell: (90.3, 127.065, 114.165, 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      63     16.00
     P      57     15.00
     O    2374      8.00
     N    2171      7.00
     C    7497      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: 2.69
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2730

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 15 sheets defined
      46.7% alpha, 12.0% beta
      15 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 3.87
  Creating SS restraints...
    Processing helix  chain 'C' and resid 39 through 44
    Processing helix  chain 'C' and resid 44 through 55
      removed outlier: 4.116A  pdb=" N   ARG C  48 " --> pdb=" O   GLU C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 93
    Processing helix  chain 'C' and resid 97 through 102
      removed outlier: 3.511A  pdb=" N   LEU C 101 " --> pdb=" O   LEU C  98 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA C 102 " --> pdb=" O   THR C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 132
    Processing helix  chain 'C' and resid 142 through 147
    Processing helix  chain 'C' and resid 159 through 170
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 3.791A  pdb=" N   ASP C 193 " --> pdb=" O   ASP C 190 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE C 194 " --> pdb=" O   TRP C 191 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 190 through 194'
    Processing helix  chain 'C' and resid 197 through 205
      removed outlier: 3.519A  pdb=" N   ALA C 203 " --> pdb=" O   HIS C 199 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL C 205 " --> pdb=" O   LYS C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 235
      removed outlier: 4.137A  pdb=" N   SER C 232 " --> pdb=" O   ALA C 228 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   THR C 233 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU C 234 " --> pdb=" O   ARG C 230 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU C 235 " --> pdb=" O   PHE C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 254
      removed outlier: 3.785A  pdb=" N   GLU C 245 " --> pdb=" O   THR C 241 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE C 249 " --> pdb=" O   GLU C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 280
    Processing helix  chain 'C' and resid 289 through 294
    Processing helix  chain 'C' and resid 308 through 315
      removed outlier: 3.613A  pdb=" N   LEU C 312 " --> pdb=" O   ASN C 308 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   THR C 314 " --> pdb=" O   GLN C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 321
    Processing helix  chain 'C' and resid 366 through 371
      removed outlier: 3.873A  pdb=" N   TYR C 370 " --> pdb=" O   ARG C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 382
    Processing helix  chain 'C' and resid 392 through 398
    Processing helix  chain 'C' and resid 406 through 422
    Processing helix  chain 'C' and resid 444 through 458
    Processing helix  chain 'C' and resid 461 through 466
      removed outlier: 3.522A  pdb=" N   HIS C 466 " --> pdb=" O   ALA C 462 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 468 through 479
    Processing helix  chain 'C' and resid 487 through 494
      removed outlier: 3.808A  pdb=" N   SER C 494 " --> pdb=" O   GLN C 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 56
      removed outlier: 4.518A  pdb=" N   ASP D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 93
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.520A  pdb=" N   ASN D 100 " --> pdb=" O   PRO D  97 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 132
    Processing helix  chain 'D' and resid 142 through 148
      removed outlier: 3.850A  pdb=" N   LEU D 148 " --> pdb=" O   ALA D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 169
      removed outlier: 3.674A  pdb=" N   VAL D 163 " --> pdb=" O   ASN D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 194
      removed outlier: 3.639A  pdb=" N   ASP D 193 " --> pdb=" O   ASP D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 211
    Processing helix  chain 'D' and resid 223 through 232
      removed outlier: 4.146A  pdb=" N   SER D 232 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 252
    Processing helix  chain 'D' and resid 275 through 280
    Processing helix  chain 'D' and resid 289 through 294
      removed outlier: 3.746A  pdb=" N   ALA D 294 " --> pdb=" O   GLU D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 307
    Processing helix  chain 'D' and resid 308 through 315
      removed outlier: 3.838A  pdb=" N   THR D 314 " --> pdb=" O   GLN D 310 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU D 315 " --> pdb=" O   VAL D 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 315 through 322
      removed outlier: 3.516A  pdb=" N   GLU D 320 " --> pdb=" O   ARG D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 374
      removed outlier: 3.744A  pdb=" N   LEU D 374 " --> pdb=" O   TYR D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 375 through 380
    Processing helix  chain 'D' and resid 392 through 398
    Processing helix  chain 'D' and resid 406 through 425
    Processing helix  chain 'D' and resid 428 through 432
      removed outlier: 3.768A  pdb=" N   LEU D 432 " --> pdb=" O   ASN D 429 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 433 through 441
    Processing helix  chain 'D' and resid 444 through 458
      removed outlier: 3.897A  pdb=" N   PHE D 450 " --> pdb=" O   GLU D 446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 461 through 479
      removed outlier: 3.659A  pdb=" N   HIS D 466 " --> pdb=" O   ALA D 462 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 485 through 495
      removed outlier: 3.794A  pdb=" N   SER D 494 " --> pdb=" O   GLN D 490 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR D 495 " --> pdb=" O   GLN D 491 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 44
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 4.250A  pdb=" N   ARG E  48 " --> pdb=" O   GLU E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 93
    Processing helix  chain 'E' and resid 122 through 132
    Processing helix  chain 'E' and resid 142 through 147
    Processing helix  chain 'E' and resid 148 through 150
      No H-bonds generated for 'chain 'E' and resid 148 through 150'
    Processing helix  chain 'E' and resid 159 through 170
    Processing helix  chain 'E' and resid 190 through 194
    Processing helix  chain 'E' and resid 198 through 211
    Processing helix  chain 'E' and resid 224 through 232
      removed outlier: 3.695A  pdb=" N   ARG E 230 " --> pdb=" O   MET E 226 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER E 232 " --> pdb=" O   ALA E 228 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 239 through 254
    Processing helix  chain 'E' and resid 289 through 294
    Processing helix  chain 'E' and resid 310 through 315
    Processing helix  chain 'E' and resid 315 through 322
      removed outlier: 3.752A  pdb=" N   GLU E 320 " --> pdb=" O   ARG E 316 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 373
      removed outlier: 4.616A  pdb=" N   TYR E 370 " --> pdb=" O   ARG E 366 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LEU E 371 " --> pdb=" O   ILE E 367 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 375 through 380
    Processing helix  chain 'E' and resid 393 through 397
      removed outlier: 3.907A  pdb=" N   ILE E 397 " --> pdb=" O   GLU E 394 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 406 through 425
    Processing helix  chain 'E' and resid 428 through 432
      removed outlier: 3.522A  pdb=" N   LEU E 432 " --> pdb=" O   ASN E 429 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 435 through 440
    Processing helix  chain 'E' and resid 445 through 458
      removed outlier: 3.803A  pdb=" N   LEU E 451 " --> pdb=" O   GLU E 447 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG E 452 " --> pdb=" O   GLN E 448 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU E 453 " --> pdb=" O   LEU E 449 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 461 through 479
    Processing helix  chain 'E' and resid 485 through 493
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 12
      removed outlier: 3.730A  pdb=" N   VAL C  15 " --> pdb=" O   ILE C  12 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLU C  22 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   THR C  33 " --> pdb=" O   VAL C  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 104 through 106
      removed outlier: 6.328A  pdb=" N   LEU C 136 " --> pdb=" O   PHE C 155 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   ALA C 157 " --> pdb=" O   LEU C 136 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   ILE C 138 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 110
      removed outlier: 3.647A  pdb=" N   GLU C 109 " --> pdb=" O   ARG C 117 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 267 through 268
      removed outlier: 6.601A  pdb=" N   ARG C 268 " --> pdb=" O   PHE C 300 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   ASP C 302 " --> pdb=" O   ARG C 268 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY C 218 " --> pdb=" O   MET C 345 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   LEU C 215 " --> pdb=" O   VAL C 386 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ILE C 388 " --> pdb=" O   LEU C 215 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER C 217 " --> pdb=" O   ILE C 388 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 326 through 327
      removed outlier: 3.543A  pdb=" N   ILE C 326 " --> pdb=" O   ILE C 333 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 12
      removed outlier: 5.473A  pdb=" N   SER D  31 " --> pdb=" O   ILE D  65 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL D  67 " --> pdb=" O   SER D  31 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   THR D  33 " --> pdb=" O   VAL D  67 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   LEU D  69 " --> pdb=" O   THR D  33 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 104 through 106
      removed outlier: 6.043A  pdb=" N   LEU D 136 " --> pdb=" O   PHE D 155 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   ALA D 157 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ILE D 138 " --> pdb=" O   ALA D 157 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 109 through 110
      removed outlier: 4.018A  pdb=" N   GLU D 109 " --> pdb=" O   ARG D 117 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 267 through 268
      removed outlier: 6.529A  pdb=" N   ARG D 268 " --> pdb=" O   PHE D 300 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LEU D 215 " --> pdb=" O   VAL D 386 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   ILE D 388 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   SER D 217 " --> pdb=" O   ILE D 388 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 326 through 327
      removed outlier: 3.740A  pdb=" N   ILE D 326 " --> pdb=" O   ILE D 333 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE D 333 " --> pdb=" O   ILE D 326 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 12
      removed outlier: 5.901A  pdb=" N   SER E  31 " --> pdb=" O   ILE E  65 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   VAL E  67 " --> pdb=" O   SER E  31 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   THR E  33 " --> pdb=" O   VAL E  67 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   LEU E  69 " --> pdb=" O   THR E  33 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL E  35 " --> pdb=" O   LEU E  69 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 105 through 106
      removed outlier: 6.542A  pdb=" N   GLU E 105 " --> pdb=" O   ILE E 137 " (cutoff:3.500A)
      removed outlier: 8.565A  pdb=" N   ALA E 139 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LEU E 136 " --> pdb=" O   PHE E 155 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   ALA E 157 " --> pdb=" O   LEU E 136 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE E 138 " --> pdb=" O   ALA E 157 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 110
      removed outlier: 3.615A  pdb=" N   GLU E 109 " --> pdb=" O   ARG E 117 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 267 through 268
      removed outlier: 6.503A  pdb=" N   ARG E 268 " --> pdb=" O   PHE E 300 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LEU E 299 " --> pdb=" O   ILE E 342 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ALA E 344 " --> pdb=" O   LEU E 299 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LEU E 301 " --> pdb=" O   ALA E 344 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ILE E 214 " --> pdb=" O   ALA E 343 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   MET E 345 " --> pdb=" O   ILE E 214 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   LEU E 216 " --> pdb=" O   MET E 345 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU E 215 " --> pdb=" O   VAL E 386 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'E' and resid 323 through 327

    433 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      30 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 3.97

  Time building geometry restraints manager: 3.23 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: 3760
        1.34 -     1.46: 1799
        1.46 -     1.58: 6721
        1.58 -     1.70: 112
        1.70 -     1.82: 99
  Bond restraints: 12491
  Sorted by residual:
  bond pdb=" O3A ANP D 601 "
       pdb=" PB  ANP D 601 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.29e+01
  bond pdb=" O3A ANP C 601 "
       pdb=" PB  ANP C 601 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.14e+01
  bond pdb=" O3A ANP C 602 "
       pdb=" PB  ANP C 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.560  0.140 2.00e-02 2.50e+03 4.88e+01
  bond pdb=" N3B ANP C 601 "
       pdb=" PG  ANP C 601 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" N3B ANP D 601 "
       pdb=" PG  ANP D 601 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.70e+01
  ... (remaining 12486 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.56: 17007
        3.56 -     7.13: 108
        7.13 -    10.69: 9
       10.69 -    14.25: 4
       14.25 -    17.81: 3
  Bond angle restraints: 17131
  Sorted by residual:
  angle pdb=" PB  ANP C 601 "
        pdb=" N3B ANP C 601 "
        pdb=" PG  ANP C 601 "
      ideal   model   delta    sigma   weight residual
     126.95  109.14   17.81 3.00e+00 1.11e-01 3.53e+01
  angle pdb=" PB  ANP C 602 "
        pdb=" N3B ANP C 602 "
        pdb=" PG  ANP C 602 "
      ideal   model   delta    sigma   weight residual
     126.95  109.34   17.61 3.00e+00 1.11e-01 3.45e+01
  angle pdb=" PB  ANP D 601 "
        pdb=" N3B ANP D 601 "
        pdb=" PG  ANP D 601 "
      ideal   model   delta    sigma   weight residual
     126.95  109.68   17.27 3.00e+00 1.11e-01 3.32e+01
  angle pdb=" C2' ANP C 601 "
        pdb=" C1' ANP C 601 "
        pdb=" N9  ANP C 601 "
      ideal   model   delta    sigma   weight residual
     112.01  123.79  -11.78 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" N   ILE D 123 "
        pdb=" CA  ILE D 123 "
        pdb=" CB  ILE D 123 "
      ideal   model   delta    sigma   weight residual
     110.50  112.84   -2.34 6.30e-01 2.52e+00 1.38e+01
  ... (remaining 17126 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.18: 6607
       21.18 -    42.35: 786
       42.35 -    63.53: 231
       63.53 -    84.70: 33
       84.70 -   105.88: 6
  Dihedral angle restraints: 7663
    sinusoidal: 3480
      harmonic: 4183
  Sorted by residual:
  dihedral pdb=" CA  GLY C  70 "
           pdb=" C   GLY C  70 "
           pdb=" N   PRO C  71 "
           pdb=" CA  PRO C  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  122.92   57.08     0      5.00e+00 4.00e-02 1.30e+02
  dihedral pdb=" CA  LEU E 189 "
           pdb=" C   LEU E 189 "
           pdb=" N   ASP E 190 "
           pdb=" CA  ASP E 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.77   25.23     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  ARG C 467 "
           pdb=" C   ARG C 467 "
           pdb=" N   LEU C 468 "
           pdb=" CA  LEU C 468 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.91   25.09     0      5.00e+00 4.00e-02 2.52e+01
  ... (remaining 7660 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.185: 1973
       0.185 -    0.369: 3
       0.369 -    0.553: 0
       0.553 -    0.738: 0
       0.738 -    0.922: 1
  Chirality restraints: 1977
  Sorted by residual:
  chirality pdb=" C1' ANP C 601 "
            pdb=" C2' ANP C 601 "
            pdb=" N9  ANP C 601 "
            pdb=" O4' ANP C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    1.50    0.92 2.00e-01 2.50e+01 2.13e+01
  chirality pdb=" C3' ANP C 601 "
            pdb=" C2' ANP C 601 "
            pdb=" C4' ANP C 601 "
            pdb=" O3' ANP C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" C3' ANP D 601 "
            pdb=" C2' ANP D 601 "
            pdb=" C4' ANP D 601 "
            pdb=" O3' ANP D 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.62    0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1974 not shown)

  Planarity restraints: 2035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 285 "    0.058 5.00e-02 4.00e+02   8.56e-02 1.17e+01
        pdb=" N   PRO E 286 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO E 286 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO E 286 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 452 "   -0.210 9.50e-02 1.11e+02   9.42e-02 5.83e+00
        pdb=" NE  ARG E 452 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 452 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 452 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 452 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT Y  25 "    0.024 2.00e-02 2.50e+03   1.17e-02 3.42e+00
        pdb=" N1   DT Y  25 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2   DT Y  25 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DT Y  25 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DT Y  25 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DT Y  25 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4   DT Y  25 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DT Y  25 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT Y  25 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DT Y  25 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2032 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 268
        2.65 -     3.22: 12044
        3.22 -     3.78: 18683
        3.78 -     4.34: 25817
        4.34 -     4.90: 41934
  Nonbonded interactions: 98746
  Sorted by model distance:
  nonbonded pdb=" O   ARG E 253 "
            pdb=" NH1 ARG E 253 "
     model   vdw
     2.093 3.120
  nonbonded pdb=" O   ASN C 346 "
            pdb=" OH  TYR C 370 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OE1 GLU D  22 "
            pdb=" ND2 ASN D  68 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" ND1 HIS C 212 "
            pdb=" OD2 ASP C 383 "
     model   vdw
     2.132 3.120
  nonbonded pdb=" O   GLU D 412 "
            pdb=" OG1 THR D 415 "
     model   vdw
     2.178 3.040
  ... (remaining 98741 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
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 1 through 180 or resid 187 through 500))
  selection = (chain 'D' and resid 1 through 500)
  selection = chain 'E'
}

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:             95.770
  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:          0.550
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.290
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.050
  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:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  133.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
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      :  0.005   0.145  12491  Z= 0.220
  Angle     :  0.771  17.814  17131  Z= 0.371
  Chirality :  0.045   0.922   1977
  Planarity :  0.005   0.094   2035
  Dihedral  : 19.419 105.879   4933
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.13 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 18.97 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    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: -0.95 (0.24), residues: 1430
  helix:  0.15 (0.22), residues: 606
  sheet: -1.36 (0.34), residues: 235
  loop : -1.00 (0.28), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 262 
 HIS   0.006   0.001   HIS C 272 
 PHE   0.017   0.001   PHE D 259 
 TYR   0.009   0.001   TYR C 187 
 ARG   0.011   0.000   ARG E 452 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16511 (  463)
  hydrogen bonds       : angle       7.04753 ( 1311)
  covalent geometry    : bond        0.00467 (12491)
  covalent geometry    : angle       0.77105 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 112
  average time/residue: 0.2568
  time to fit residues: 42.0582
Evaluate side-chains
  96 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   69 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 75 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 116 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 134 optimal weight:    0.0370
   overall best weight:    1.1262

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

Flipped N/Q/H residues before XYZ refinement:
C 202 ASN
** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 HIS
C 340 GLN
C 448 GLN
** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 400 ASN
D 406 GLN
D 421 GLN
D 500 HIS
E 271 HIS
E 284 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.091373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.062476 restraints weight = 35786.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 4.10
r_work: 0.2837 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12491  Z= 0.158
  Angle     :  0.703   9.443  17131  Z= 0.359
  Chirality :  0.042   0.214   1977
  Planarity :  0.005   0.064   2035
  Dihedral  : 18.743 135.681   2190
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.06 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.23 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    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: -0.67 (0.24), residues: 1430
  helix:  0.39 (0.22), residues: 628
  sheet: -1.02 (0.34), residues: 237
  loop : -1.01 (0.28), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 191 
 HIS   0.005   0.001   HIS C 272 
 PHE   0.021   0.001   PHE D 259 
 TYR   0.012   0.002   TYR D 187 
 ARG   0.007   0.001   ARG E 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04477 (  463)
  hydrogen bonds       : angle       5.27721 ( 1311)
  covalent geometry    : bond        0.00365 (12491)
  covalent geometry    : angle       0.70269 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8872 (mm-40)
REVERT: C  256 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8256 (mm)
REVERT: C  370 TYR cc_start: 0.8379 (t80) cc_final: 0.8101 (t80)
REVERT: C  397 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9286 (mp)
REVERT: D  213 SER cc_start: 0.8993 (m) cc_final: 0.8263 (p)
REVERT: D  345 MET cc_start: 0.8464 (ptm) cc_final: 0.8203 (tmm)
REVERT: D  380 ASP cc_start: 0.9411 (OUTLIER) cc_final: 0.9046 (m-30)
REVERT: D  417 MET cc_start: 0.9295 (mmm) cc_final: 0.8914 (mmt)
REVERT: D  455 MET cc_start: 0.9428 (mmm) cc_final: 0.9120 (tpt)
REVERT: E   39 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9035 (mt-10)
REVERT: E  151 HIS cc_start: 0.7817 (t70) cc_final: 0.7599 (t70)
REVERT: E  227 MET cc_start: 0.9434 (mtp) cc_final: 0.9209 (mpp)
REVERT: E  370 TYR cc_start: 0.8327 (t80) cc_final: 0.8098 (t80)
REVERT: E  448 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8597 (pp30)
  outliers start: 30
  outliers final: 12
  residues processed: 134
  average time/residue: 0.2850
  time to fit residues: 59.7472
Evaluate side-chains
  108 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 2.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  500 HIS
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  448 GLN
Chi-restraints excluded: chain E residue  468 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 144 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 107 optimal weight:    0.0670
   chunk 147 optimal weight:    8.9990
   overall best weight:    2.9524

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

Flipped N/Q/H residues before XYZ refinement:
** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 340 GLN
D 500 HIS
E  95 GLN
E 140 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.088232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.059653 restraints weight = 36699.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 4.05
r_work: 0.2772 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  12491  Z= 0.264
  Angle     :  0.732   8.724  17131  Z= 0.371
  Chirality :  0.042   0.202   1977
  Planarity :  0.005   0.065   2035
  Dihedral  : 18.738 132.413   2190
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  7.34 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.23 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.19 %
    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: -0.71 (0.23), residues: 1430
  helix:  0.30 (0.22), residues: 645
  sheet: -0.97 (0.36), residues: 205
  loop : -1.05 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 191 
 HIS   0.020   0.001   HIS D 500 
 PHE   0.024   0.002   PHE D 259 
 TYR   0.016   0.002   TYR C 187 
 ARG   0.003   0.000   ARG C 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04783 (  463)
  hydrogen bonds       : angle       5.17052 ( 1311)
  covalent geometry    : bond        0.00593 (12491)
  covalent geometry    : angle       0.73151 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 96
  time to evaluate  : 1.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8915 (mm-40)
REVERT: C  145 GLU cc_start: 0.8551 (mp0) cc_final: 0.8272 (mp0)
REVERT: C  256 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8476 (mm)
REVERT: C  310 GLN cc_start: 0.9432 (mm-40) cc_final: 0.9128 (mm-40)
REVERT: C  370 TYR cc_start: 0.8473 (t80) cc_final: 0.8226 (t80)
REVERT: C  397 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9305 (mp)
REVERT: D    1 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (tpt)
REVERT: D  213 SER cc_start: 0.9150 (m) cc_final: 0.8486 (p)
REVERT: D  313 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9007 (mm-30)
REVERT: D  380 ASP cc_start: 0.9436 (OUTLIER) cc_final: 0.9099 (m-30)
REVERT: D  417 MET cc_start: 0.9320 (mmm) cc_final: 0.8716 (mmt)
REVERT: D  455 MET cc_start: 0.9363 (mmm) cc_final: 0.9039 (tpt)
REVERT: E   39 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8997 (mt-10)
REVERT: E  227 MET cc_start: 0.9437 (mtp) cc_final: 0.9209 (mpp)
REVERT: E  370 TYR cc_start: 0.8497 (t80) cc_final: 0.8192 (t80)
  outliers start: 44
  outliers final: 20
  residues processed: 132
  average time/residue: 0.2445
  time to fit residues: 50.0440
Evaluate side-chains
  113 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  500 HIS
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  252 ILE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  460 LEU
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  474 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 126 optimal weight:    5.9990
   chunk 132 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 128 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 418 HIS
D 130 HIS
D 500 HIS
E  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.088227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.059236 restraints weight = 36165.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 4.08
r_work: 0.2774 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12491  Z= 0.215
  Angle     :  0.672   8.225  17131  Z= 0.343
  Chirality :  0.041   0.171   1977
  Planarity :  0.004   0.064   2035
  Dihedral  : 18.766 134.551   2188
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.27 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.39 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.23), residues: 1430
  helix:  0.43 (0.21), residues: 647
  sheet: -0.72 (0.37), residues: 200
  loop : -1.09 (0.28), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 191 
 HIS   0.023   0.001   HIS D 500 
 PHE   0.016   0.001   PHE D 259 
 TYR   0.017   0.002   TYR C 187 
 ARG   0.002   0.000   ARG E 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  463)
  hydrogen bonds       : angle       4.91330 ( 1311)
  covalent geometry    : bond        0.00493 (12491)
  covalent geometry    : angle       0.67229 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 99
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8921 (mm-40)
REVERT: C  145 GLU cc_start: 0.8578 (mp0) cc_final: 0.8269 (mp0)
REVERT: C  171 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9128 (p)
REVERT: C  187 TYR cc_start: 0.8374 (m-80) cc_final: 0.8131 (m-80)
REVERT: C  256 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (mm)
REVERT: C  271 HIS cc_start: 0.8165 (t-90) cc_final: 0.7824 (t70)
REVERT: C  310 GLN cc_start: 0.9434 (mm-40) cc_final: 0.9170 (mm-40)
REVERT: C  370 TYR cc_start: 0.8478 (t80) cc_final: 0.8188 (t80)
REVERT: C  397 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9312 (mp)
REVERT: C  449 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9296 (pp)
REVERT: C  496 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8694 (tppp)
REVERT: D  112 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8762 (mp)
REVERT: D  213 SER cc_start: 0.9126 (m) cc_final: 0.8795 (p)
REVERT: D  313 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9059 (mm-30)
REVERT: D  345 MET cc_start: 0.8536 (ptm) cc_final: 0.8258 (tmm)
REVERT: D  370 TYR cc_start: 0.9133 (t80) cc_final: 0.8794 (t80)
REVERT: D  380 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9103 (m-30)
REVERT: D  417 MET cc_start: 0.9455 (mmm) cc_final: 0.9002 (mmt)
REVERT: D  455 MET cc_start: 0.9369 (mmm) cc_final: 0.9041 (tpt)
REVERT: D  478 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8806 (ttm)
REVERT: E   39 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9009 (mt-10)
REVERT: E  227 MET cc_start: 0.9411 (mtp) cc_final: 0.9195 (mpp)
REVERT: E  370 TYR cc_start: 0.8603 (t80) cc_final: 0.8289 (t80)
  outliers start: 44
  outliers final: 21
  residues processed: 132
  average time/residue: 0.2031
  time to fit residues: 41.1437
Evaluate side-chains
  124 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  397 ILE
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  496 LYS
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  478 MET
Chi-restraints excluded: chain D residue  500 HIS
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  252 ILE
Chi-restraints excluded: chain E residue  258 ASP
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  397 ILE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  460 LEU
Chi-restraints excluded: chain E residue  468 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 138 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 123 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 421 GLN
D 500 HIS
E  95 GLN
E 199 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.087046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.058558 restraints weight = 36658.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 4.06
r_work: 0.2752 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  12491  Z= 0.275
  Angle     :  0.712  12.685  17131  Z= 0.362
  Chirality :  0.042   0.161   1977
  Planarity :  0.005   0.060   2035
  Dihedral  : 18.865 135.720   2188
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  8.04 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.56 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.23), residues: 1430
  helix:  0.46 (0.21), residues: 647
  sheet: -0.78 (0.37), residues: 199
  loop : -1.14 (0.28), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 191 
 HIS   0.007   0.001   HIS D 500 
 PHE   0.016   0.001   PHE D 259 
 TYR   0.015   0.002   TYR C 187 
 ARG   0.004   0.000   ARG C 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04542 (  463)
  hydrogen bonds       : angle       4.95822 ( 1311)
  covalent geometry    : bond        0.00626 (12491)
  covalent geometry    : angle       0.71174 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 98
  time to evaluate  : 1.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8972 (mm-40)
REVERT: C   44 GLU cc_start: 0.8745 (pm20) cc_final: 0.8469 (pm20)
REVERT: C  145 GLU cc_start: 0.8606 (mp0) cc_final: 0.8270 (mp0)
REVERT: C  187 TYR cc_start: 0.8437 (m-80) cc_final: 0.8215 (m-80)
REVERT: C  256 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8459 (mm)
REVERT: C  271 HIS cc_start: 0.8310 (t70) cc_final: 0.8098 (t-90)
REVERT: C  310 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9190 (mm-40)
REVERT: C  370 TYR cc_start: 0.8498 (t80) cc_final: 0.8180 (t80)
REVERT: C  391 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7653 (tt)
REVERT: C  449 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9316 (pp)
REVERT: C  496 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8750 (tppp)
REVERT: D    1 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8468 (tpt)
REVERT: D  103 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.8518 (t0)
REVERT: D  112 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8840 (mp)
REVERT: D  213 SER cc_start: 0.9185 (m) cc_final: 0.8860 (p)
REVERT: D  313 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9053 (mm-30)
REVERT: D  380 ASP cc_start: 0.9446 (OUTLIER) cc_final: 0.9129 (m-30)
REVERT: D  417 MET cc_start: 0.9440 (mmm) cc_final: 0.8986 (mmt)
REVERT: D  455 MET cc_start: 0.9368 (mmm) cc_final: 0.9059 (tpt)
REVERT: D  478 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8822 (ttm)
REVERT: E   39 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8985 (mt-10)
REVERT: E  370 TYR cc_start: 0.8645 (t80) cc_final: 0.8342 (t80)
  outliers start: 52
  outliers final: 26
  residues processed: 140
  average time/residue: 0.3913
  time to fit residues: 83.2773
Evaluate side-chains
  128 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 1.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  408 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  496 LYS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  348 CYS
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  478 MET
Chi-restraints excluded: chain E residue   95 GLN
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  252 ILE
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  397 ILE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  460 LEU
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  474 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 145 optimal weight:    8.9990
   chunk 99 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
C 421 GLN
E  95 GLN
E 199 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.088355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.059786 restraints weight = 36536.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 4.10
r_work: 0.2790 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12491  Z= 0.164
  Angle     :  0.658  12.039  17131  Z= 0.333
  Chirality :  0.040   0.258   1977
  Planarity :  0.004   0.061   2035
  Dihedral  : 18.844 137.901   2188
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  6.92 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.05 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.24), residues: 1430
  helix:  0.62 (0.21), residues: 650
  sheet: -0.84 (0.36), residues: 226
  loop : -1.02 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 191 
 HIS   0.004   0.001   HIS E 418 
 PHE   0.014   0.001   PHE D 259 
 TYR   0.012   0.001   TYR C 187 
 ARG   0.005   0.000   ARG C 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  463)
  hydrogen bonds       : angle       4.70959 ( 1311)
  covalent geometry    : bond        0.00380 (12491)
  covalent geometry    : angle       0.65841 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8979 (mm-40)
REVERT: C   44 GLU cc_start: 0.8717 (pm20) cc_final: 0.8438 (pm20)
REVERT: C  145 GLU cc_start: 0.8610 (mp0) cc_final: 0.8265 (mp0)
REVERT: C  187 TYR cc_start: 0.8409 (m-80) cc_final: 0.8197 (m-80)
REVERT: C  255 LYS cc_start: 0.8046 (ptmm) cc_final: 0.7638 (ptmm)
REVERT: C  256 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8460 (mm)
REVERT: C  271 HIS cc_start: 0.8284 (t70) cc_final: 0.8040 (t-90)
REVERT: C  310 GLN cc_start: 0.9422 (mm-40) cc_final: 0.9172 (mm-40)
REVERT: C  370 TYR cc_start: 0.8505 (t80) cc_final: 0.8176 (t80)
REVERT: C  391 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7562 (tt)
REVERT: C  449 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9334 (pp)
REVERT: D    1 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8447 (tpt)
REVERT: D   44 GLU cc_start: 0.7631 (mp0) cc_final: 0.7410 (mp0)
REVERT: D  103 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.8532 (t0)
REVERT: D  112 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8749 (mp)
REVERT: D  213 SER cc_start: 0.9135 (m) cc_final: 0.8806 (p)
REVERT: D  313 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9046 (mm-30)
REVERT: D  317 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8626 (tm-30)
REVERT: D  345 MET cc_start: 0.8727 (ptm) cc_final: 0.8266 (tmm)
REVERT: D  380 ASP cc_start: 0.9436 (OUTLIER) cc_final: 0.9118 (m-30)
REVERT: D  417 MET cc_start: 0.9423 (mmm) cc_final: 0.9008 (mmt)
REVERT: D  455 MET cc_start: 0.9405 (mmm) cc_final: 0.9091 (tpt)
REVERT: D  478 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8823 (ttm)
REVERT: E   39 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9023 (mt-10)
REVERT: E  370 TYR cc_start: 0.8681 (t80) cc_final: 0.8375 (t80)
REVERT: E  478 MET cc_start: 0.8790 (ttm) cc_final: 0.8450 (mtp)
  outliers start: 43
  outliers final: 21
  residues processed: 133
  average time/residue: 0.1939
  time to fit residues: 40.0194
Evaluate side-chains
  130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  259 PHE
Chi-restraints excluded: chain D residue  317 GLU
Chi-restraints excluded: chain D residue  348 CYS
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  478 MET
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  397 ILE
Chi-restraints excluded: chain E residue  460 LEU
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  474 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 89 optimal weight:    0.3980
   chunk 135 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:    0.1980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
E  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.087932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.059026 restraints weight = 36391.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 4.15
r_work: 0.2783 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12491  Z= 0.172
  Angle     :  0.660  12.259  17131  Z= 0.331
  Chirality :  0.040   0.239   1977
  Planarity :  0.004   0.059   2035
  Dihedral  : 18.836 138.824   2188
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  7.27 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.70 %
    Favored  : 76.85 %
  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: -0.32 (0.24), residues: 1430
  helix:  0.73 (0.22), residues: 644
  sheet: -0.75 (0.36), residues: 226
  loop : -0.99 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E 191 
 HIS   0.003   0.001   HIS C 272 
 PHE   0.013   0.001   PHE C 307 
 TYR   0.012   0.001   TYR C 187 
 ARG   0.003   0.000   ARG E 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  463)
  hydrogen bonds       : angle       4.59121 ( 1311)
  covalent geometry    : bond        0.00397 (12491)
  covalent geometry    : angle       0.65972 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 105
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9006 (mm-40)
REVERT: C   44 GLU cc_start: 0.8740 (pm20) cc_final: 0.8466 (pm20)
REVERT: C  145 GLU cc_start: 0.8644 (mp0) cc_final: 0.8281 (mp0)
REVERT: C  255 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7679 (ptmm)
REVERT: C  256 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8451 (mm)
REVERT: C  271 HIS cc_start: 0.8361 (t70) cc_final: 0.7876 (t-90)
REVERT: C  310 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9175 (mm-40)
REVERT: C  370 TYR cc_start: 0.8507 (t80) cc_final: 0.8190 (t80)
REVERT: C  391 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7540 (tt)
REVERT: C  417 MET cc_start: 0.9009 (mmm) cc_final: 0.8643 (mmm)
REVERT: C  449 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9335 (pp)
REVERT: C  467 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8006 (ptp90)
REVERT: D    1 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (tpt)
REVERT: D   44 GLU cc_start: 0.7658 (mp0) cc_final: 0.7432 (mp0)
REVERT: D  103 ASN cc_start: 0.9356 (OUTLIER) cc_final: 0.8566 (t0)
REVERT: D  213 SER cc_start: 0.9184 (m) cc_final: 0.8861 (p)
REVERT: D  317 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (tm-30)
REVERT: D  345 MET cc_start: 0.8737 (ptm) cc_final: 0.8258 (tmm)
REVERT: D  380 ASP cc_start: 0.9436 (OUTLIER) cc_final: 0.9159 (m-30)
REVERT: D  417 MET cc_start: 0.9408 (mmm) cc_final: 0.8992 (mmt)
REVERT: D  455 MET cc_start: 0.9425 (mmm) cc_final: 0.9089 (tpt)
REVERT: D  478 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8817 (ttm)
REVERT: E   39 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9038 (mt-10)
REVERT: E  370 TYR cc_start: 0.8701 (t80) cc_final: 0.8456 (t80)
  outliers start: 42
  outliers final: 23
  residues processed: 139
  average time/residue: 0.2258
  time to fit residues: 48.6372
Evaluate side-chains
  132 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  467 ARG
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  317 GLU
Chi-restraints excluded: chain D residue  319 LEU
Chi-restraints excluded: chain D residue  348 CYS
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  478 MET
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  391 LEU
Chi-restraints excluded: chain E residue  397 ILE
Chi-restraints excluded: chain E residue  460 LEU
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  474 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 118 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 125 optimal weight:    5.9990
   chunk 147 optimal weight:   10.0000
   chunk 132 optimal weight:    4.9990
   chunk 130 optimal weight:    8.9990
   chunk 135 optimal weight:    0.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** E  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.087899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.058707 restraints weight = 36796.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 4.19
r_work: 0.2778 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12491  Z= 0.181
  Angle     :  0.685  13.202  17131  Z= 0.344
  Chirality :  0.041   0.227   1977
  Planarity :  0.004   0.059   2035
  Dihedral  : 18.877 138.400   2188
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  6.92 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.69 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1430
  helix:  0.75 (0.22), residues: 645
  sheet: -0.66 (0.36), residues: 227
  loop : -0.93 (0.29), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E 191 
 HIS   0.003   0.001   HIS E 151 
 PHE   0.013   0.001   PHE C 307 
 TYR   0.011   0.001   TYR C 187 
 ARG   0.003   0.000   ARG C 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  463)
  hydrogen bonds       : angle       4.59341 ( 1311)
  covalent geometry    : bond        0.00418 (12491)
  covalent geometry    : angle       0.68542 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9000 (mm-40)
REVERT: C   44 GLU cc_start: 0.8735 (pm20) cc_final: 0.8483 (pm20)
REVERT: C   69 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9308 (pp)
REVERT: C  145 GLU cc_start: 0.8639 (mp0) cc_final: 0.8256 (mp0)
REVERT: C  255 LYS cc_start: 0.8138 (ptmm) cc_final: 0.7658 (ptmm)
REVERT: C  256 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8383 (mm)
REVERT: C  271 HIS cc_start: 0.8353 (t70) cc_final: 0.7835 (t-90)
REVERT: C  310 GLN cc_start: 0.9417 (mm-40) cc_final: 0.9190 (mm-40)
REVERT: C  370 TYR cc_start: 0.8508 (t80) cc_final: 0.8174 (t80)
REVERT: C  391 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7494 (tt)
REVERT: C  449 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9346 (pp)
REVERT: C  496 LYS cc_start: 0.8886 (tppt) cc_final: 0.8675 (tppt)
REVERT: D    1 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8424 (tpt)
REVERT: D   44 GLU cc_start: 0.7639 (mp0) cc_final: 0.7423 (mp0)
REVERT: D  103 ASN cc_start: 0.9379 (OUTLIER) cc_final: 0.8574 (t0)
REVERT: D  213 SER cc_start: 0.9161 (m) cc_final: 0.8829 (p)
REVERT: D  313 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9116 (mm-30)
REVERT: D  317 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8590 (tm-30)
REVERT: D  345 MET cc_start: 0.8707 (ptm) cc_final: 0.8330 (tmm)
REVERT: D  380 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.9168 (m-30)
REVERT: D  417 MET cc_start: 0.9407 (mmm) cc_final: 0.8988 (mmt)
REVERT: D  455 MET cc_start: 0.9402 (mmm) cc_final: 0.9087 (tpt)
REVERT: D  478 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8799 (ttm)
REVERT: E   39 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9018 (mt-10)
REVERT: E  370 TYR cc_start: 0.8717 (t80) cc_final: 0.8469 (t80)
  outliers start: 37
  outliers final: 23
  residues processed: 132
  average time/residue: 0.2056
  time to fit residues: 41.6635
Evaluate side-chains
  130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  317 GLU
Chi-restraints excluded: chain D residue  319 LEU
Chi-restraints excluded: chain D residue  348 CYS
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  478 MET
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  391 LEU
Chi-restraints excluded: chain E residue  397 ILE
Chi-restraints excluded: chain E residue  460 LEU
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  474 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 79 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0870
   chunk 98 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0470
   chunk 90 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0270
   overall best weight:    0.4114

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

Flipped N/Q/H residues before XYZ refinement:
C 497 GLN
E  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.090216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.061585 restraints weight = 36213.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 4.23
r_work: 0.2848 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12491  Z= 0.120
  Angle     :  0.667  14.741  17131  Z= 0.332
  Chirality :  0.040   0.154   1977
  Planarity :  0.004   0.061   2035
  Dihedral  : 18.713 138.759   2188
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  6.29 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.43 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1430
  helix:  1.03 (0.22), residues: 631
  sheet: -0.53 (0.37), residues: 228
  loop : -0.78 (0.29), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 191 
 HIS   0.004   0.001   HIS C 272 
 PHE   0.011   0.001   PHE C 307 
 TYR   0.009   0.001   TYR E 465 
 ARG   0.004   0.000   ARG E 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03147 (  463)
  hydrogen bonds       : angle       4.28842 ( 1311)
  covalent geometry    : bond        0.00272 (12491)
  covalent geometry    : angle       0.66735 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8970 (mm-40)
REVERT: C   44 GLU cc_start: 0.8782 (pm20) cc_final: 0.8410 (pm20)
REVERT: C  145 GLU cc_start: 0.8602 (mp0) cc_final: 0.8193 (mp0)
REVERT: C  187 TYR cc_start: 0.8376 (m-80) cc_final: 0.8173 (m-80)
REVERT: C  271 HIS cc_start: 0.8327 (t70) cc_final: 0.8001 (t-90)
REVERT: C  310 GLN cc_start: 0.9390 (mm-40) cc_final: 0.9178 (mm-40)
REVERT: C  370 TYR cc_start: 0.8501 (t80) cc_final: 0.8170 (t80)
REVERT: C  391 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7321 (tt)
REVERT: C  417 MET cc_start: 0.9001 (mmm) cc_final: 0.8738 (mmm)
REVERT: C  449 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9348 (pp)
REVERT: D    1 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8438 (tpt)
REVERT: D  213 SER cc_start: 0.9118 (m) cc_final: 0.8458 (p)
REVERT: D  313 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9031 (mm-30)
REVERT: D  345 MET cc_start: 0.8475 (ptm) cc_final: 0.8267 (tmm)
REVERT: D  370 TYR cc_start: 0.8751 (t80) cc_final: 0.8359 (t80)
REVERT: D  380 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.9074 (m-30)
REVERT: D  422 MET cc_start: 0.9258 (mmm) cc_final: 0.8970 (mmm)
REVERT: D  455 MET cc_start: 0.9435 (mmm) cc_final: 0.9117 (tpt)
REVERT: D  478 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8848 (ttm)
REVERT: E   39 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9048 (mt-10)
  outliers start: 28
  outliers final: 16
  residues processed: 128
  average time/residue: 0.2039
  time to fit residues: 40.5294
Evaluate side-chains
  127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain C residue  486 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue  259 PHE
Chi-restraints excluded: chain D residue  348 CYS
Chi-restraints excluded: chain D residue  371 LEU
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain D residue  478 MET
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  391 LEU
Chi-restraints excluded: chain E residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 100 optimal weight:    0.0070
   chunk 74 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 139 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0030
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.5208

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

Flipped N/Q/H residues before XYZ refinement:
** C 272 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 = 0.3701 r_free = 0.3701 target = 0.090442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.061648 restraints weight = 36135.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 4.22
r_work: 0.2850 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12491  Z= 0.120
  Angle     :  0.672  15.113  17131  Z= 0.331
  Chirality :  0.040   0.208   1977
  Planarity :  0.004   0.060   2035
  Dihedral  : 18.656 139.743   2188
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.43 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.25 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1430
  helix:  1.03 (0.22), residues: 631
  sheet: -0.40 (0.37), residues: 226
  loop : -0.78 (0.28), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 191 
 HIS   0.008   0.001   HIS D 418 
 PHE   0.012   0.001   PHE C 307 
 TYR   0.011   0.001   TYR E 370 
 ARG   0.003   0.000   ARG E 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03148 (  463)
  hydrogen bonds       : angle       4.29742 ( 1311)
  covalent geometry    : bond        0.00274 (12491)
  covalent geometry    : angle       0.67221 (17131)

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

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

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2860 Ramachandran restraints generated.
    1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8981 (mm-40)
REVERT: C   44 GLU cc_start: 0.8800 (pm20) cc_final: 0.8373 (pm20)
REVERT: C  145 GLU cc_start: 0.8421 (mp0) cc_final: 0.7993 (mp0)
REVERT: C  187 TYR cc_start: 0.8363 (m-80) cc_final: 0.8140 (m-80)
REVERT: C  271 HIS cc_start: 0.8303 (t70) cc_final: 0.7971 (t-90)
REVERT: C  310 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9182 (mm-40)
REVERT: C  370 TYR cc_start: 0.8493 (t80) cc_final: 0.8166 (t80)
REVERT: C  391 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7342 (tt)
REVERT: C  417 MET cc_start: 0.8958 (mmm) cc_final: 0.8667 (mmm)
REVERT: C  422 MET cc_start: 0.9377 (mmm) cc_final: 0.9081 (mmm)
REVERT: C  449 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9348 (pp)
REVERT: D    1 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8397 (tpt)
REVERT: D  213 SER cc_start: 0.9116 (m) cc_final: 0.8423 (p)
REVERT: D  313 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9072 (mm-30)
REVERT: D  380 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.9067 (m-30)
REVERT: D  422 MET cc_start: 0.9293 (mmm) cc_final: 0.9021 (mmm)
REVERT: D  455 MET cc_start: 0.9405 (mmm) cc_final: 0.9117 (tpt)
REVERT: E   39 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9064 (mt-10)
  outliers start: 22
  outliers final: 13
  residues processed: 121
  average time/residue: 0.2049
  time to fit residues: 38.6210
Evaluate side-chains
  120 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  374 LEU
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  449 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue  348 CYS
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  403 LEU
Chi-restraints excluded: chain E residue  187 TYR
Chi-restraints excluded: chain E residue  232 SER
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  259 PHE
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  391 LEU
Chi-restraints excluded: chain E residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 121 optimal weight:    0.0030
   chunk 18 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 123 optimal weight:    0.0030
   chunk 108 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.5402

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

Flipped N/Q/H residues before XYZ refinement:
** C 272 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 = 0.3711 r_free = 0.3711 target = 0.090840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.062283 restraints weight = 36252.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 4.22
r_work: 0.2864 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12491  Z= 0.119
  Angle     :  0.669  14.822  17131  Z= 0.328
  Chirality :  0.039   0.170   1977
  Planarity :  0.004   0.060   2035
  Dihedral  : 18.562 138.747   2188
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.29 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 21.67 %
    Favored  : 76.35 %
  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:  0.12 (0.24), residues: 1430
  helix:  1.07 (0.22), residues: 631
  sheet: -0.38 (0.37), residues: 226
  loop : -0.76 (0.28), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 191 
 HIS   0.003   0.001   HIS C 272 
 PHE   0.016   0.001   PHE C 307 
 TYR   0.011   0.002   TYR E 370 
 ARG   0.003   0.000   ARG E 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02996 (  463)
  hydrogen bonds       : angle       4.20885 ( 1311)
  covalent geometry    : bond        0.00275 (12491)
  covalent geometry    : angle       0.66936 (17131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7498.75 seconds
wall clock time: 135 minutes 13.14 seconds (8113.14 seconds total)