Starting phenix.real_space_refine
on Wed Jul 30 03:34:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vc2_43130/07_2025/8vc2_43130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vc2_43130/07_2025/8vc2_43130.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vc2_43130/07_2025/8vc2_43130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vc2_43130/07_2025/8vc2_43130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vc2_43130/07_2025/8vc2_43130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vc2_43130/07_2025/8vc2_43130.cif"
  }
  resolution = 3.98
  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=   0.002 sd=   0.025
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       4      5.49       5
     S     120      5.16       5
     C    7720      2.51       5
     N    1932      2.21       5
     O    2020      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11796
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2918
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 367}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'PSC': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'PSC:plan-4': 1, 'PSC:plan-3': 1}
          Unresolved non-hydrogen planarities: 6
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 6.91, per 1000 atoms: 0.59
  Number of scatterers: 11796
  At special positions: 0
  Unit cell: (103.75, 103.75, 96.28, 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     120     16.00
     P       4     15.00
     O    2020      8.00
     N    1932      7.00
     C    7720      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: 3.50
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2856

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      85.5% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 32
    Processing helix  chain 'A' and resid 51 through 79
    Processing helix  chain 'A' and resid 89 through 112
      removed outlier: 3.669A  pdb=" N   VAL A 102 " --> pdb=" O   CYS A  98 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   VAL A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 135
      removed outlier: 4.555A  pdb=" N   GLU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLU A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 175
      removed outlier: 4.070A  pdb=" N   GLU A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 230
      removed outlier: 3.533A  pdb=" N   TYR A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   GLY A 188 " --> pdb=" O   THR A 184 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   PHE A 189 " --> pdb=" O   ASN A 185 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE A 191 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER A 226 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 340
      removed outlier: 5.042A  pdb=" N   GLY A 292 " --> pdb=" O   CYS A 288 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   CYS A 302 " --> pdb=" O   ARG A 298 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   LEU A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
      Proline residue:  A 315  - end of helix
      removed outlier: 3.635A  pdb=" N   LEU A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      Proline residue:  A 331  - end of helix
    Processing helix  chain 'A' and resid 344 through 390
      removed outlier: 4.128A  pdb=" N   MET A 362 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      Proline residue:  A 368  - end of helix
      removed outlier: 3.724A  pdb=" N   GLU A 375 " --> pdb=" O   TYR A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 410
      removed outlier: 3.983A  pdb=" N   MET A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 419
    Processing helix  chain 'A' and resid 424 through 446
      removed outlier: 3.650A  pdb=" N   VAL A 428 " --> pdb=" O   ARG A 424 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 439 " --> pdb=" O   THR A 435 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE A 444 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 32
    Processing helix  chain 'B' and resid 51 through 79
    Processing helix  chain 'B' and resid 89 through 112
      removed outlier: 3.669A  pdb=" N   VAL B 102 " --> pdb=" O   CYS B  98 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   VAL B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 135
      removed outlier: 4.555A  pdb=" N   GLU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ASN B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU B 134 " --> pdb=" O   ALA B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 175
      removed outlier: 4.070A  pdb=" N   GLU B 144 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE B 154 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 230
      removed outlier: 3.533A  pdb=" N   TYR B 186 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   GLY B 188 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   PHE B 189 " --> pdb=" O   ASN B 185 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE B 191 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR B 224 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER B 226 " --> pdb=" O   ASN B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 340
      removed outlier: 5.042A  pdb=" N   GLY B 292 " --> pdb=" O   CYS B 288 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   CYS B 302 " --> pdb=" O   ARG B 298 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   LEU B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
      Proline residue:  B 315  - end of helix
      removed outlier: 3.633A  pdb=" N   LEU B 320 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      Proline residue:  B 331  - end of helix
    Processing helix  chain 'B' and resid 344 through 390
      removed outlier: 4.129A  pdb=" N   MET B 362 " --> pdb=" O   HIS B 358 " (cutoff:3.500A)
      Proline residue:  B 368  - end of helix
      removed outlier: 3.724A  pdb=" N   GLU B 375 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 410
      removed outlier: 3.982A  pdb=" N   MET B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 419
    Processing helix  chain 'B' and resid 424 through 446
      removed outlier: 3.650A  pdb=" N   VAL B 428 " --> pdb=" O   ARG B 424 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL B 439 " --> pdb=" O   THR B 435 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE B 444 " --> pdb=" O   ILE B 440 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN B 445 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 32
    Processing helix  chain 'C' and resid 51 through 79
    Processing helix  chain 'C' and resid 89 through 112
      removed outlier: 3.668A  pdb=" N   VAL C 102 " --> pdb=" O   CYS C  98 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL C 103 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 135
      removed outlier: 4.555A  pdb=" N   GLU C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN C 127 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU C 134 " --> pdb=" O   ALA C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 175
      removed outlier: 4.069A  pdb=" N   GLU C 144 " --> pdb=" O   SER C 140 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE C 154 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 230
      removed outlier: 3.533A  pdb=" N   TYR C 186 " --> pdb=" O   ILE C 182 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   GLY C 188 " --> pdb=" O   THR C 184 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   PHE C 189 " --> pdb=" O   ASN C 185 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE C 191 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG C 211 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR C 224 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER C 226 " --> pdb=" O   ASN C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 340
      removed outlier: 5.042A  pdb=" N   GLY C 292 " --> pdb=" O   CYS C 288 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   CYS C 302 " --> pdb=" O   ARG C 298 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR C 305 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   LEU C 314 " --> pdb=" O   ASP C 310 " (cutoff:3.500A)
      Proline residue:  C 315  - end of helix
      removed outlier: 3.634A  pdb=" N   LEU C 320 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      Proline residue:  C 331  - end of helix
    Processing helix  chain 'C' and resid 344 through 390
      removed outlier: 4.128A  pdb=" N   MET C 362 " --> pdb=" O   HIS C 358 " (cutoff:3.500A)
      Proline residue:  C 368  - end of helix
      removed outlier: 3.724A  pdb=" N   GLU C 375 " --> pdb=" O   TYR C 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 410
      removed outlier: 3.983A  pdb=" N   MET C 408 " --> pdb=" O   SER C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 419
    Processing helix  chain 'C' and resid 424 through 446
      removed outlier: 3.650A  pdb=" N   VAL C 428 " --> pdb=" O   ARG C 424 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR C 436 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL C 439 " --> pdb=" O   THR C 435 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE C 444 " --> pdb=" O   ILE C 440 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN C 445 " --> pdb=" O   LEU C 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 32
    Processing helix  chain 'D' and resid 51 through 79
    Processing helix  chain 'D' and resid 89 through 112
      removed outlier: 3.668A  pdb=" N   VAL D 102 " --> pdb=" O   CYS D  98 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 135
      removed outlier: 4.556A  pdb=" N   GLU D 126 " --> pdb=" O   LEU D 122 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ASN D 127 " --> pdb=" O   SER D 123 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU D 134 " --> pdb=" O   ALA D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 175
      removed outlier: 4.070A  pdb=" N   GLU D 144 " --> pdb=" O   SER D 140 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU D 153 " --> pdb=" O   ALA D 149 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE D 154 " --> pdb=" O   LEU D 150 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU D 155 " --> pdb=" O   LEU D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 230
      removed outlier: 3.533A  pdb=" N   TYR D 186 " --> pdb=" O   ILE D 182 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   GLY D 188 " --> pdb=" O   THR D 184 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   PHE D 189 " --> pdb=" O   ASN D 185 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU D 208 " --> pdb=" O   ALA D 204 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG D 211 " --> pdb=" O   ALA D 207 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR D 224 " --> pdb=" O   ALA D 220 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA D 225 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER D 226 " --> pdb=" O   ASN D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 340
      removed outlier: 5.042A  pdb=" N   GLY D 292 " --> pdb=" O   CYS D 288 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   CYS D 302 " --> pdb=" O   ARG D 298 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR D 305 " --> pdb=" O   LEU D 301 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   LEU D 314 " --> pdb=" O   ASP D 310 " (cutoff:3.500A)
      Proline residue:  D 315  - end of helix
      removed outlier: 3.633A  pdb=" N   LEU D 320 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
      Proline residue:  D 331  - end of helix
    Processing helix  chain 'D' and resid 344 through 390
      removed outlier: 4.129A  pdb=" N   MET D 362 " --> pdb=" O   HIS D 358 " (cutoff:3.500A)
      Proline residue:  D 368  - end of helix
      removed outlier: 3.725A  pdb=" N   GLU D 375 " --> pdb=" O   TYR D 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 410
      removed outlier: 3.983A  pdb=" N   MET D 408 " --> pdb=" O   SER D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 415 through 419
    Processing helix  chain 'D' and resid 424 through 446
      removed outlier: 3.651A  pdb=" N   VAL D 428 " --> pdb=" O   ARG D 424 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   THR D 436 " --> pdb=" O   GLY D 432 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL D 439 " --> pdb=" O   THR D 435 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE D 444 " --> pdb=" O   ILE D 440 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN D 445 " --> pdb=" O   LEU D 441 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19
    Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 19
    Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 19

    988 hydrogen bonds defined for protein.
    2940 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.14

  Time building geometry restraints manager: 4.01 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1752
        1.30 -     1.43: 3008
        1.43 -     1.56: 7016
        1.56 -     1.69: 56
        1.69 -     1.81: 180
  Bond restraints: 12012
  Sorted by residual:
  bond pdb=" C1  PSC C 501 "
       pdb=" O01 PSC C 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.443 -0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C1  PSC B 501 "
       pdb=" O01 PSC B 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.443 -0.112 2.00e-02 2.50e+03 3.11e+01
  bond pdb=" C1  PSC D 501 "
       pdb=" O01 PSC D 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.442 -0.111 2.00e-02 2.50e+03 3.09e+01
  bond pdb=" C1  PSC A 501 "
       pdb=" O01 PSC A 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.441 -0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" C19 PSC B 501 "
       pdb=" O03 PSC B 501 "
    ideal  model  delta    sigma   weight residual
    1.326  1.426 -0.100 2.00e-02 2.50e+03 2.51e+01
  ... (remaining 12007 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.36: 16188
        3.36 -     6.71: 92
        6.71 -    10.07: 4
       10.07 -    13.43: 8
       13.43 -    16.78: 4
  Bond angle restraints: 16296
  Sorted by residual:
  angle pdb=" O11 PSC B 501 "
        pdb=" P   PSC B 501 "
        pdb=" O12 PSC B 501 "
      ideal   model   delta    sigma   weight residual
      93.08  109.86  -16.78 3.00e+00 1.11e-01 3.13e+01
  angle pdb=" O11 PSC D 501 "
        pdb=" P   PSC D 501 "
        pdb=" O12 PSC D 501 "
      ideal   model   delta    sigma   weight residual
      93.08  109.86  -16.78 3.00e+00 1.11e-01 3.13e+01
  angle pdb=" O11 PSC C 501 "
        pdb=" P   PSC C 501 "
        pdb=" O12 PSC C 501 "
      ideal   model   delta    sigma   weight residual
      93.08  109.85  -16.77 3.00e+00 1.11e-01 3.13e+01
  angle pdb=" O11 PSC A 501 "
        pdb=" P   PSC A 501 "
        pdb=" O12 PSC A 501 "
      ideal   model   delta    sigma   weight residual
      93.08  109.85  -16.77 3.00e+00 1.11e-01 3.12e+01
  angle pdb=" C2  PSC A 501 "
        pdb=" C1  PSC A 501 "
        pdb=" O01 PSC A 501 "
      ideal   model   delta    sigma   weight residual
     111.06  121.59  -10.53 3.00e+00 1.11e-01 1.23e+01
  ... (remaining 16291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.84: 6877
       23.84 -    47.68: 223
       47.68 -    71.53: 76
       71.53 -    95.37: 8
       95.37 -   119.21: 4
  Dihedral angle restraints: 7188
    sinusoidal: 2764
      harmonic: 4424
  Sorted by residual:
  dihedral pdb=" CA  LEU C 135 "
           pdb=" C   LEU C 135 "
           pdb=" N   GLY C 136 "
           pdb=" CA  GLY C 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.00   23.00     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  LEU A 135 "
           pdb=" C   LEU A 135 "
           pdb=" N   GLY A 136 "
           pdb=" CA  GLY A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.01   22.99     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  LEU B 135 "
           pdb=" C   LEU B 135 "
           pdb=" N   GLY B 136 "
           pdb=" CA  GLY B 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.02   22.98     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 7185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1294
       0.029 -    0.058: 527
       0.058 -    0.087: 133
       0.087 -    0.116: 46
       0.116 -    0.144: 16
  Chirality restraints: 2016
  Sorted by residual:
  chirality pdb=" C02 PSC A 501 "
            pdb=" C01 PSC A 501 "
            pdb=" C03 PSC A 501 "
            pdb=" O01 PSC A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.37    2.51   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  TYR C 124 "
            pdb=" N   TYR C 124 "
            pdb=" C   TYR C 124 "
            pdb=" CB  TYR C 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  TYR B 124 "
            pdb=" N   TYR B 124 "
            pdb=" C   TYR B 124 "
            pdb=" CB  TYR B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 2013 not shown)

  Planarity restraints: 1956
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 309 "   -0.017 2.00e-02 2.50e+03   3.34e-02 1.12e+01
        pdb=" C   ALA B 309 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ALA B 309 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP B 310 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 309 "   -0.017 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   ALA C 309 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ALA C 309 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP C 310 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 309 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   ALA D 309 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ALA D 309 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASP D 310 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1953 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 3829
        2.86 -     3.37: 12927
        3.37 -     3.88: 19578
        3.88 -     4.39: 21966
        4.39 -     4.90: 36502
  Nonbonded interactions: 94802
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 165 "
            pdb=" NE1 TRP A 354 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OD2 ASP B 165 "
            pdb=" NE1 TRP B 354 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OD2 ASP D 165 "
            pdb=" NE1 TRP D 354 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OD2 ASP C 165 "
            pdb=" NE1 TRP C 354 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" OE2 GLU A  76 "
            pdb=" ND2 ASN A 185 "
     model   vdw
     2.363 3.120
  ... (remaining 94797 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.900
  Find NCS groups from input model:        0.280
  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:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
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      :  0.006   0.112  12012  Z= 0.295
  Angle     :  0.843  16.784  16296  Z= 0.468
  Chirality :  0.036   0.144   2016
  Planarity :  0.010   0.087   1956
  Dihedral  : 14.087 119.212   4332
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.18 %
    Favored  : 98.51 %
  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: -0.98 (0.20), residues: 1500
  helix: -0.33 (0.14), residues: 1232
  sheet:  0.54 (0.71), residues: 48
  loop : -1.91 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.007   TRP D 354 
 HIS   0.008   0.003   HIS D 358 
 PHE   0.010   0.002   PHE C 203 
 TYR   0.037   0.006   TYR B 124 
 ARG   0.019   0.003   ARG D 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09684 (  988)
  hydrogen bonds       : angle       5.48264 ( 2940)
  covalent geometry    : bond        0.00558 (12012)
  covalent geometry    : angle       0.84302 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 449
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.7062 (mmm) cc_final: 0.6758 (mmt)
REVERT: A  197 MET cc_start: 0.7610 (mmm) cc_final: 0.7155 (tmm)
REVERT: A  401 GLU cc_start: 0.7893 (tt0) cc_final: 0.7297 (tt0)
REVERT: A  404 SER cc_start: 0.8411 (p) cc_final: 0.8001 (t)
REVERT: B  167 CYS cc_start: 0.7256 (m) cc_final: 0.6814 (t)
REVERT: B  197 MET cc_start: 0.7666 (mmm) cc_final: 0.7313 (tmm)
REVERT: B  384 CYS cc_start: 0.5109 (m) cc_final: 0.4103 (m)
REVERT: B  401 GLU cc_start: 0.7990 (tt0) cc_final: 0.7256 (tt0)
REVERT: B  404 SER cc_start: 0.8480 (p) cc_final: 0.8124 (t)
REVERT: C  167 CYS cc_start: 0.7238 (m) cc_final: 0.6838 (t)
REVERT: C  197 MET cc_start: 0.7604 (mmm) cc_final: 0.7259 (tmm)
REVERT: C  384 CYS cc_start: 0.5188 (m) cc_final: 0.4764 (m)
REVERT: C  401 GLU cc_start: 0.7925 (tt0) cc_final: 0.7317 (tt0)
REVERT: C  404 SER cc_start: 0.8485 (p) cc_final: 0.8156 (t)
REVERT: D  167 CYS cc_start: 0.7256 (m) cc_final: 0.6819 (t)
REVERT: D  197 MET cc_start: 0.7618 (mmm) cc_final: 0.7283 (tmm)
REVERT: D  384 CYS cc_start: 0.5078 (m) cc_final: 0.4742 (m)
REVERT: D  401 GLU cc_start: 0.7859 (tt0) cc_final: 0.7290 (tt0)
REVERT: D  404 SER cc_start: 0.8483 (p) cc_final: 0.8119 (t)
  outliers start: 4
  outliers final: 1
  residues processed: 453
  average time/residue: 0.2276
  time to fit residues: 147.5838
Evaluate side-chains
  298 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 297
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 112 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 70 optimal weight:    0.5980
   chunk 86 optimal weight:   40.0000
   chunk 134 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.226188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.190639 restraints weight = 12779.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.196469 restraints weight = 7913.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.200719 restraints weight = 5598.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12012  Z= 0.150
  Angle     :  0.649  10.264  16296  Z= 0.330
  Chirality :  0.037   0.126   2016
  Planarity :  0.004   0.043   1956
  Dihedral  :  8.704  67.786   1750
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 14.31 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.22), residues: 1500
  helix:  1.38 (0.14), residues: 1264
  sheet:  0.05 (0.70), residues: 48
  loop : -0.82 (0.50), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 193 
 HIS   0.003   0.001   HIS B 326 
 PHE   0.016   0.002   PHE C 203 
 TYR   0.018   0.002   TYR D 124 
 ARG   0.003   0.000   ARG A 344 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04692 (  988)
  hydrogen bonds       : angle       3.95718 ( 2940)
  covalent geometry    : bond        0.00330 (12012)
  covalent geometry    : angle       0.64935 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 321
  time to evaluate  : 1.659 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7568 (mp)
REVERT: A  179 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7402 (pm20)
REVERT: A  197 MET cc_start: 0.7786 (mmm) cc_final: 0.7438 (tmm)
REVERT: B   26 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7587 (mp)
REVERT: B  125 MET cc_start: 0.6801 (mmt) cc_final: 0.6518 (tpt)
REVERT: B  346 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7008 (t-90)
REVERT: C   26 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7556 (mp)
REVERT: C  179 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7011 (pm20)
REVERT: C  297 MET cc_start: 0.7327 (mpp) cc_final: 0.6935 (mpp)
REVERT: C  346 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7013 (t-90)
REVERT: C  401 GLU cc_start: 0.8279 (tt0) cc_final: 0.7723 (tt0)
REVERT: D   26 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7577 (mp)
REVERT: D  179 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7066 (pm20)
REVERT: D  346 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7010 (t-90)
REVERT: D  401 GLU cc_start: 0.8262 (tt0) cc_final: 0.7626 (tt0)
  outliers start: 63
  outliers final: 30
  residues processed: 362
  average time/residue: 0.2272
  time to fit residues: 119.6545
Evaluate side-chains
  288 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 250
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  179 GLN
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  395 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 132 optimal weight:    8.9990
   chunk 143 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 144 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 358 HIS
B 358 HIS
C 358 HIS
D 358 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.228055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.191985 restraints weight = 13009.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.197464 restraints weight = 8272.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.201438 restraints weight = 5917.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12012  Z= 0.140
  Angle     :  0.652  12.170  16296  Z= 0.320
  Chirality :  0.038   0.193   2016
  Planarity :  0.004   0.053   1956
  Dihedral  :  7.732  55.648   1748
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 18.87 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.22), residues: 1500
  helix:  1.75 (0.14), residues: 1268
  sheet:  0.24 (0.75), residues: 48
  loop : -0.80 (0.50), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 193 
 HIS   0.003   0.001   HIS A 358 
 PHE   0.012   0.001   PHE C 203 
 TYR   0.016   0.001   TYR A 124 
 ARG   0.005   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  988)
  hydrogen bonds       : angle       3.83808 ( 2940)
  covalent geometry    : bond        0.00314 (12012)
  covalent geometry    : angle       0.65185 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 273
  time to evaluate  : 1.320 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7570 (mp)
REVERT: A   27 LYS cc_start: 0.7533 (tttt) cc_final: 0.7154 (tmtt)
REVERT: A  171 MET cc_start: 0.7928 (tmm) cc_final: 0.7698 (tmm)
REVERT: A  197 MET cc_start: 0.7747 (mmm) cc_final: 0.7486 (tmm)
REVERT: A  297 MET cc_start: 0.7174 (mpp) cc_final: 0.6686 (mpp)
REVERT: B   26 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7596 (mp)
REVERT: B   27 LYS cc_start: 0.7480 (tttt) cc_final: 0.7128 (tttm)
REVERT: B  297 MET cc_start: 0.7116 (mpp) cc_final: 0.6613 (mpp)
REVERT: B  346 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7003 (t-90)
REVERT: B  443 GLN cc_start: 0.7853 (tt0) cc_final: 0.7352 (tt0)
REVERT: C   26 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7614 (mp)
REVERT: C   27 LYS cc_start: 0.7549 (tttt) cc_final: 0.7242 (tttm)
REVERT: C   67 ILE cc_start: 0.8859 (tp) cc_final: 0.8527 (tt)
REVERT: C  121 MET cc_start: 0.7818 (tmm) cc_final: 0.7604 (tmm)
REVERT: C  179 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7027 (pm20)
REVERT: C  346 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.6996 (t-90)
REVERT: D   26 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7631 (mp)
REVERT: D   27 LYS cc_start: 0.7634 (tttt) cc_final: 0.7327 (tttm)
REVERT: D   38 ARG cc_start: 0.7742 (ptm-80) cc_final: 0.7541 (ptm-80)
REVERT: D  179 GLN cc_start: 0.7510 (tm-30) cc_final: 0.6956 (pm20)
REVERT: D  182 ILE cc_start: 0.8506 (mt) cc_final: 0.8238 (mt)
REVERT: D  346 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7011 (t-90)
  outliers start: 54
  outliers final: 34
  residues processed: 307
  average time/residue: 0.2217
  time to fit residues: 98.9454
Evaluate side-chains
  287 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 246
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 124 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 147 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 133 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 134 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 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 = 0.4495 r_free = 0.4495 target = 0.224131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.187041 restraints weight = 13023.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.192341 restraints weight = 8339.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.195923 restraints weight = 6078.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12012  Z= 0.141
  Angle     :  0.631  12.428  16296  Z= 0.310
  Chirality :  0.037   0.160   2016
  Planarity :  0.004   0.056   1956
  Dihedral  :  7.333  50.146   1748
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 18.87 %
    Favored  : 75.39 %
  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:  2.35 (0.22), residues: 1500
  helix:  1.95 (0.14), residues: 1268
  sheet:  0.02 (0.75), residues: 48
  loop : -0.68 (0.50), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 193 
 HIS   0.003   0.001   HIS D 326 
 PHE   0.011   0.001   PHE A  39 
 TYR   0.016   0.001   TYR A 124 
 ARG   0.004   0.000   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04299 (  988)
  hydrogen bonds       : angle       3.81677 ( 2940)
  covalent geometry    : bond        0.00328 (12012)
  covalent geometry    : angle       0.63077 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 279
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7611 (mp)
REVERT: A  121 MET cc_start: 0.7605 (tmm) cc_final: 0.7328 (tmm)
REVERT: A  197 MET cc_start: 0.7743 (mmm) cc_final: 0.7504 (tpt)
REVERT: A  332 TYR cc_start: 0.7439 (t80) cc_final: 0.7236 (t80)
REVERT: B   26 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7678 (mp)
REVERT: B   67 ILE cc_start: 0.8878 (tp) cc_final: 0.8571 (tt)
REVERT: B  121 MET cc_start: 0.7836 (tmm) cc_final: 0.7579 (tmm)
REVERT: B  346 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7030 (t-90)
REVERT: C   26 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7732 (mp)
REVERT: C   67 ILE cc_start: 0.8882 (tp) cc_final: 0.8584 (tt)
REVERT: C  121 MET cc_start: 0.7844 (tmm) cc_final: 0.7601 (tmm)
REVERT: C  179 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7251 (pm20)
REVERT: C  301 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: C  346 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7039 (t-90)
REVERT: C  443 GLN cc_start: 0.8040 (tt0) cc_final: 0.7407 (tt0)
REVERT: D   26 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7729 (mp)
REVERT: D   67 ILE cc_start: 0.8907 (tp) cc_final: 0.8575 (tt)
REVERT: D  179 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7313 (pm20)
REVERT: D  182 ILE cc_start: 0.8798 (mt) cc_final: 0.8545 (mt)
REVERT: D  346 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7038 (t-90)
REVERT: D  419 MET cc_start: 0.7762 (mtp) cc_final: 0.7467 (ttm)
  outliers start: 73
  outliers final: 49
  residues processed: 329
  average time/residue: 0.2137
  time to fit residues: 102.9286
Evaluate side-chains
  307 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 250
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  193 TRP
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  193 TRP
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  359 LEU
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  193 TRP
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  427 ILE
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 128 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 126 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 137 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 370 HIS
** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.219708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.181960 restraints weight = 13102.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.186572 restraints weight = 8829.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.189475 restraints weight = 6670.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.4461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12012  Z= 0.173
  Angle     :  0.688  12.268  16296  Z= 0.333
  Chirality :  0.039   0.160   2016
  Planarity :  0.005   0.054   1956
  Dihedral  :  7.228  52.013   1748
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 20.36 %
    Favored  : 73.82 %
  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:  2.36 (0.22), residues: 1500
  helix:  2.06 (0.14), residues: 1256
  sheet: -0.18 (0.73), residues: 48
  loop : -1.27 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 326 
 PHE   0.010   0.001   PHE A  39 
 TYR   0.015   0.001   TYR D 124 
 ARG   0.005   0.000   ARG D 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  988)
  hydrogen bonds       : angle       3.94243 ( 2940)
  covalent geometry    : bond        0.00423 (12012)
  covalent geometry    : angle       0.68782 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 277
  time to evaluate  : 1.363 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7688 (mp)
REVERT: A  178 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7613 (ptt180)
REVERT: A  332 TYR cc_start: 0.7636 (t80) cc_final: 0.7282 (t80)
REVERT: A  362 MET cc_start: 0.7059 (tmm) cc_final: 0.6819 (tmm)
REVERT: B   26 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7775 (mp)
REVERT: B  346 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7030 (t-90)
REVERT: C   26 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (mp)
REVERT: C   27 LYS cc_start: 0.7538 (tttt) cc_final: 0.6769 (tmtt)
REVERT: C  121 MET cc_start: 0.7864 (tmm) cc_final: 0.7477 (tmm)
REVERT: C  346 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7007 (t-90)
REVERT: C  401 GLU cc_start: 0.8422 (tt0) cc_final: 0.7826 (tt0)
REVERT: C  443 GLN cc_start: 0.8113 (tt0) cc_final: 0.7119 (tt0)
REVERT: D   26 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7794 (mp)
REVERT: D  179 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7456 (pp30)
REVERT: D  346 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7009 (t-90)
  outliers start: 74
  outliers final: 58
  residues processed: 330
  average time/residue: 0.2228
  time to fit residues: 105.8393
Evaluate side-chains
  312 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 247
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  193 TRP
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 LEU
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  400 LEU
Chi-restraints excluded: chain C residue  408 MET
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  193 TRP
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  395 VAL
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 116 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 124 optimal weight:    0.6980
   chunk 142 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
A 443 GLN
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.223415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.188698 restraints weight = 13204.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.191015 restraints weight = 9103.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.193370 restraints weight = 7170.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12012  Z= 0.141
  Angle     :  0.663  11.780  16296  Z= 0.321
  Chirality :  0.038   0.167   2016
  Planarity :  0.004   0.055   1956
  Dihedral  :  7.109  52.982   1748
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 20.91 %
    Favored  : 73.51 %
  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:  2.66 (0.22), residues: 1500
  helix:  2.27 (0.15), residues: 1256
  sheet: -0.14 (0.74), residues: 48
  loop : -1.19 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 326 
 PHE   0.009   0.001   PHE A  39 
 TYR   0.018   0.001   TYR D 124 
 ARG   0.005   0.000   ARG D 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  988)
  hydrogen bonds       : angle       3.78568 ( 2940)
  covalent geometry    : bond        0.00327 (12012)
  covalent geometry    : angle       0.66262 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 260
  time to evaluate  : 1.279 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7641 (mp)
REVERT: A   27 LYS cc_start: 0.7317 (tttt) cc_final: 0.6919 (tmtt)
REVERT: A  121 MET cc_start: 0.7563 (tmm) cc_final: 0.7322 (tmm)
REVERT: B   26 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: B  117 ARG cc_start: 0.7064 (ttm110) cc_final: 0.6381 (mtm110)
REVERT: B  346 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6867 (t-90)
REVERT: C   26 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (mp)
REVERT: C  301 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7768 (mp)
REVERT: C  346 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6841 (t-90)
REVERT: D   26 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7779 (mp)
REVERT: D  117 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6519 (mtm110)
REVERT: D  121 MET cc_start: 0.7780 (tmm) cc_final: 0.7562 (tmm)
REVERT: D  346 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.6873 (t-90)
REVERT: D  419 MET cc_start: 0.7786 (mtp) cc_final: 0.7503 (ttm)
  outliers start: 71
  outliers final: 52
  residues processed: 308
  average time/residue: 0.2328
  time to fit residues: 103.5356
Evaluate side-chains
  299 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 239
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  193 TRP
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  193 TRP
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 LEU
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain D residue  193 TRP
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 112 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 443 GLN
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 HIS
B 443 GLN
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.223581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.185239 restraints weight = 13163.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.190116 restraints weight = 8672.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.193225 restraints weight = 6469.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.4987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12012  Z= 0.140
  Angle     :  0.698  12.665  16296  Z= 0.326
  Chirality :  0.038   0.166   2016
  Planarity :  0.004   0.056   1956
  Dihedral  :  6.971  53.462   1748
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 21.46 %
    Favored  : 72.88 %
  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:  2.70 (0.22), residues: 1500
  helix:  2.32 (0.15), residues: 1256
  sheet: -0.44 (0.72), residues: 48
  loop : -1.28 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 193 
 HIS   0.003   0.001   HIS C 392 
 PHE   0.008   0.001   PHE A  39 
 TYR   0.017   0.001   TYR D 124 
 ARG   0.006   0.000   ARG C 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  988)
  hydrogen bonds       : angle       3.76228 ( 2940)
  covalent geometry    : bond        0.00329 (12012)
  covalent geometry    : angle       0.69764 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 245
  time to evaluate  : 1.274 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7549 (mp)
REVERT: A  117 ARG cc_start: 0.7090 (ttm110) cc_final: 0.6864 (ttp-110)
REVERT: A  121 MET cc_start: 0.7514 (tmm) cc_final: 0.7289 (tmm)
REVERT: A  216 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7664 (tt)
REVERT: B   26 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7697 (mp)
REVERT: B   27 LYS cc_start: 0.7366 (tttt) cc_final: 0.6982 (tptt)
REVERT: B  121 MET cc_start: 0.7524 (tmm) cc_final: 0.7270 (tmm)
REVERT: B  346 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.6951 (t-90)
REVERT: C   26 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7581 (mp)
REVERT: C  121 MET cc_start: 0.7584 (tmm) cc_final: 0.7318 (tmm)
REVERT: C  301 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7688 (mp)
REVERT: C  346 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6914 (t-90)
REVERT: D   26 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7652 (mp)
REVERT: D   27 LYS cc_start: 0.7399 (tttt) cc_final: 0.7052 (tptt)
REVERT: D  121 MET cc_start: 0.7696 (tmm) cc_final: 0.7426 (tmm)
REVERT: D  346 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.6933 (t-90)
  outliers start: 72
  outliers final: 56
  residues processed: 297
  average time/residue: 0.2163
  time to fit residues: 94.5892
Evaluate side-chains
  304 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 239
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  193 TRP
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  193 TRP
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 LEU
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  400 LEU
Chi-restraints excluded: chain C residue  408 MET
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain D residue  193 TRP
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  395 VAL
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 132 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 139 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 147 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS
** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.219989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.181945 restraints weight = 13147.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.186397 restraints weight = 8725.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.189954 restraints weight = 6559.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.5147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12012  Z= 0.150
  Angle     :  0.721  13.990  16296  Z= 0.335
  Chirality :  0.039   0.167   2016
  Planarity :  0.004   0.056   1956
  Dihedral  :  6.804  53.420   1748
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 22.09 %
    Favored  : 72.17 %
  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:  2.67 (0.22), residues: 1500
  helix:  2.33 (0.15), residues: 1256
  sheet: -0.64 (0.69), residues: 48
  loop : -1.46 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 193 
 HIS   0.003   0.001   HIS C 392 
 PHE   0.008   0.001   PHE A  64 
 TYR   0.015   0.001   TYR B 124 
 ARG   0.007   0.001   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  988)
  hydrogen bonds       : angle       3.81871 ( 2940)
  covalent geometry    : bond        0.00358 (12012)
  covalent geometry    : angle       0.72120 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 236
  time to evaluate  : 1.334 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7581 (mp)
REVERT: A   27 LYS cc_start: 0.7281 (tttt) cc_final: 0.6972 (tmtt)
REVERT: A   66 VAL cc_start: 0.7216 (t) cc_final: 0.7003 (t)
REVERT: A  121 MET cc_start: 0.7543 (tmm) cc_final: 0.7260 (tmm)
REVERT: A  401 GLU cc_start: 0.8401 (tt0) cc_final: 0.7984 (tt0)
REVERT: B   26 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7587 (mp)
REVERT: B  121 MET cc_start: 0.7601 (tmm) cc_final: 0.7339 (tmm)
REVERT: B  346 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.6937 (t-90)
REVERT: B  401 GLU cc_start: 0.8461 (tt0) cc_final: 0.8112 (tt0)
REVERT: C   26 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7604 (mp)
REVERT: C   27 LYS cc_start: 0.7335 (tttt) cc_final: 0.7029 (tmtt)
REVERT: C  117 ARG cc_start: 0.7174 (ttp-110) cc_final: 0.6925 (mtm110)
REVERT: C  121 MET cc_start: 0.7551 (tmm) cc_final: 0.7333 (tmm)
REVERT: C  301 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7762 (mp)
REVERT: C  346 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6896 (t-90)
REVERT: D   26 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: D  117 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6823 (mtm110)
REVERT: D  121 MET cc_start: 0.7671 (tmm) cc_final: 0.7390 (tmm)
REVERT: D  179 GLN cc_start: 0.7662 (pp30) cc_final: 0.7416 (pp30)
REVERT: D  346 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6958 (t-90)
REVERT: D  401 GLU cc_start: 0.8459 (tt0) cc_final: 0.8174 (tt0)
REVERT: D  443 GLN cc_start: 0.7545 (tt0) cc_final: 0.7254 (tt0)
  outliers start: 73
  outliers final: 61
  residues processed: 291
  average time/residue: 0.2168
  time to fit residues: 92.5103
Evaluate side-chains
  299 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 230
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  193 TRP
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  193 TRP
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 LEU
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  400 LEU
Chi-restraints excluded: chain C residue  408 MET
Chi-restraints excluded: chain C residue  428 VAL
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   39 PHE
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  193 TRP
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  395 VAL
Chi-restraints excluded: chain D residue  400 LEU
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 134 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 129 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 147 optimal weight:    0.9990
   chunk 114 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 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 = 0.4491 r_free = 0.4491 target = 0.222075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.184151 restraints weight = 13094.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.189026 restraints weight = 8636.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.192079 restraints weight = 6443.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12012  Z= 0.137
  Angle     :  0.716  14.011  16296  Z= 0.329
  Chirality :  0.038   0.171   2016
  Planarity :  0.004   0.055   1956
  Dihedral  :  6.657  55.083   1748
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 22.48 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.22), residues: 1500
  helix:  2.41 (0.15), residues: 1256
  sheet: -0.78 (0.67), residues: 48
  loop : -1.43 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.003   0.001   HIS D 326 
 PHE   0.008   0.001   PHE A  39 
 TYR   0.015   0.001   TYR D 124 
 ARG   0.007   0.000   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  988)
  hydrogen bonds       : angle       3.73580 ( 2940)
  covalent geometry    : bond        0.00321 (12012)
  covalent geometry    : angle       0.71644 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 243
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A   24 PHE cc_start: 0.7746 (t80) cc_final: 0.7124 (t80)
REVERT: A   27 LYS cc_start: 0.7060 (tttt) cc_final: 0.6741 (tmtt)
REVERT: A  117 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7019 (mtm110)
REVERT: A  121 MET cc_start: 0.7466 (tmm) cc_final: 0.7196 (tmm)
REVERT: A  332 TYR cc_start: 0.7871 (t80) cc_final: 0.7293 (t80)
REVERT: A  401 GLU cc_start: 0.8356 (tt0) cc_final: 0.8129 (tt0)
REVERT: B   26 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7590 (mp)
REVERT: B  117 ARG cc_start: 0.7131 (ttp-110) cc_final: 0.6738 (mtm110)
REVERT: B  121 MET cc_start: 0.7572 (tmm) cc_final: 0.7328 (tmm)
REVERT: B  332 TYR cc_start: 0.7801 (t80) cc_final: 0.7320 (t80)
REVERT: B  346 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7031 (t-90)
REVERT: B  401 GLU cc_start: 0.8441 (tt0) cc_final: 0.8117 (tt0)
REVERT: C   27 LYS cc_start: 0.7200 (tttt) cc_final: 0.6882 (tmtt)
REVERT: C  117 ARG cc_start: 0.7066 (ttp-110) cc_final: 0.6734 (mtm110)
REVERT: C  121 MET cc_start: 0.7575 (tmm) cc_final: 0.7287 (tmm)
REVERT: C  125 MET cc_start: 0.7332 (tpt) cc_final: 0.6956 (tpt)
REVERT: C  301 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7647 (mp)
REVERT: C  332 TYR cc_start: 0.7831 (t80) cc_final: 0.7378 (t80)
REVERT: C  346 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7001 (t-90)
REVERT: D   27 LYS cc_start: 0.7329 (tttt) cc_final: 0.7038 (tptm)
REVERT: D  121 MET cc_start: 0.7662 (tmm) cc_final: 0.7358 (tmm)
REVERT: D  332 TYR cc_start: 0.7786 (t80) cc_final: 0.7346 (t80)
REVERT: D  346 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.6993 (t-90)
REVERT: D  401 GLU cc_start: 0.8422 (tt0) cc_final: 0.8165 (tt0)
  outliers start: 65
  outliers final: 54
  residues processed: 290
  average time/residue: 0.2170
  time to fit residues: 92.0445
Evaluate side-chains
  295 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 236
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  193 TRP
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain C residue   39 PHE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  193 TRP
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  363 LEU
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  400 LEU
Chi-restraints excluded: chain C residue  408 MET
Chi-restraints excluded: chain C residue  440 ILE
Chi-restraints excluded: chain D residue   39 PHE
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain D residue  193 TRP
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 123 optimal weight:   40.0000
   chunk 131 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0980
   chunk 40 optimal weight:   20.0000
   chunk 126 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 105 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 136 optimal weight:    3.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 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 = 0.4459 r_free = 0.4459 target = 0.217775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.179290 restraints weight = 13024.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.183753 restraints weight = 8801.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.186590 restraints weight = 6712.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  12012  Z= 0.175
  Angle     :  0.756  14.383  16296  Z= 0.350
  Chirality :  0.041   0.169   2016
  Planarity :  0.004   0.053   1956
  Dihedral  :  6.665  54.430   1748
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 23.19 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.22), residues: 1500
  helix:  2.21 (0.15), residues: 1268
  sheet: -0.75 (0.68), residues: 48
  loop : -1.28 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 193 
 HIS   0.008   0.001   HIS A  22 
 PHE   0.012   0.001   PHE B  31 
 TYR   0.013   0.001   TYR D 124 
 ARG   0.007   0.001   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04356 (  988)
  hydrogen bonds       : angle       3.90461 ( 2940)
  covalent geometry    : bond        0.00432 (12012)
  covalent geometry    : angle       0.75582 (16296)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 249
  time to evaluate  : 1.258 
Fit side-chains
REVERT: A   24 PHE cc_start: 0.7907 (t80) cc_final: 0.7385 (t80)
REVERT: A   27 LYS cc_start: 0.7064 (tttt) cc_final: 0.6777 (tmtt)
REVERT: A  117 ARG cc_start: 0.7391 (ttm110) cc_final: 0.6825 (mtm110)
REVERT: A  124 TYR cc_start: 0.8025 (p90) cc_final: 0.7676 (p90)
REVERT: A  401 GLU cc_start: 0.8459 (tt0) cc_final: 0.8021 (tt0)
REVERT: B  117 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6799 (mtm110)
REVERT: B  332 TYR cc_start: 0.7904 (t80) cc_final: 0.7334 (t80)
REVERT: B  346 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7040 (t-90)
REVERT: B  401 GLU cc_start: 0.8487 (tt0) cc_final: 0.7975 (tt0)
REVERT: C   24 PHE cc_start: 0.7786 (t80) cc_final: 0.7128 (t80)
REVERT: C   27 LYS cc_start: 0.7155 (tttt) cc_final: 0.6889 (tmtt)
REVERT: C  117 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6764 (mtm110)
REVERT: C  125 MET cc_start: 0.7499 (tpt) cc_final: 0.6964 (tpt)
REVERT: C  301 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7812 (mp)
REVERT: C  332 TYR cc_start: 0.7937 (t80) cc_final: 0.7393 (t80)
REVERT: C  346 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7017 (t-90)
REVERT: D   24 PHE cc_start: 0.7875 (t80) cc_final: 0.7169 (t80)
REVERT: D   27 LYS cc_start: 0.7312 (tttt) cc_final: 0.6964 (tptt)
REVERT: D  117 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7037 (mtm110)
REVERT: D  121 MET cc_start: 0.7726 (tmm) cc_final: 0.7343 (tmm)
REVERT: D  346 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7040 (t-90)
REVERT: D  401 GLU cc_start: 0.8512 (tt0) cc_final: 0.8227 (tt0)
  outliers start: 62
  outliers final: 55
  residues processed: 292
  average time/residue: 0.2319
  time to fit residues: 97.6780
Evaluate side-chains
  302 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 243
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  193 TRP
Chi-restraints excluded: chain A residue  307 HIS
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   98 CYS
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  346 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain C residue   39 PHE
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   98 CYS
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  193 TRP
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  307 HIS
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain C residue  346 HIS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  357 THR
Chi-restraints excluded: chain C residue  364 VAL
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  400 LEU
Chi-restraints excluded: chain C residue  408 MET
Chi-restraints excluded: chain C residue  440 ILE
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain D residue  307 HIS
Chi-restraints excluded: chain D residue  346 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  363 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 THR
Chi-restraints excluded: chain D residue  428 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 59 optimal weight:    0.1980
   chunk 16 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0040
   chunk 108 optimal weight:    0.9990
   chunk 145 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 HIS
** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 HIS
** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.239420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.201761 restraints weight = 13000.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.206425 restraints weight = 8669.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.209955 restraints weight = 6526.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.5541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12012  Z= 0.130
  Angle     :  0.732  13.978  16296  Z= 0.334
  Chirality :  0.038   0.178   2016
  Planarity :  0.004   0.055   1956
  Dihedral  :  6.550  56.966   1748
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.63 %
    Favored  : 70.68 %
  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:  2.79 (0.22), residues: 1500
  helix:  2.36 (0.15), residues: 1268
  sheet: -0.77 (0.67), residues: 48
  loop : -1.18 (0.50), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 180 
 HIS   0.007   0.001   HIS B  22 
 PHE   0.011   0.001   PHE D 203 
 TYR   0.016   0.001   TYR D 124 
 ARG   0.007   0.000   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03892 (  988)
  hydrogen bonds       : angle       3.67871 ( 2940)
  covalent geometry    : bond        0.00292 (12012)
  covalent geometry    : angle       0.73205 (16296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3722.05 seconds
wall clock time: 65 minutes 33.95 seconds (3933.95 seconds total)