Starting phenix.real_space_refine
on Sat May 17 08:23:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gts_34266/05_2025/8gts_34266_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gts_34266/05_2025/8gts_34266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gts_34266/05_2025/8gts_34266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gts_34266/05_2025/8gts_34266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gts_34266/05_2025/8gts_34266_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gts_34266/05_2025/8gts_34266_neut.cif"
  }
  resolution = 3.87
  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=   0.001 sd=   0.030
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: 4
    Type Number    sf(0)   Gaussians
     S      77      5.16       5
     C   10290      2.51       5
     N    2429      2.21       5
     O    2674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15470
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2210
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 11, 'TRANS': 276}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 61
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 5.61, per 1000 atoms: 0.36
  Number of scatterers: 15470
  At special positions: 0
  Unit cell: (105.93, 108.07, 116.63, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      77     16.00
     O    2674      8.00
     N    2429      7.00
     C   10290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 246 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.83
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3934

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 7 sheets defined
      69.8% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
      removed outlier: 3.691A  pdb=" N   THR A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU A   9 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU A  45 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      Proline residue:  A  46  - end of helix
    Processing helix  chain 'A' and resid 73 through 87
    Processing helix  chain 'A' and resid 99 through 131
      removed outlier: 4.420A  pdb=" N   LEU A 103 " --> pdb=" O   GLY A  99 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      Proline residue:  A 123  - end of helix
    Processing helix  chain 'A' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE A 135 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
      removed outlier: 3.554A  pdb=" N   TYR A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 236
      removed outlier: 3.649A  pdb=" N   THR A 220 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LEU A 221 " --> pdb=" O   HIS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 255
      removed outlier: 3.975A  pdb=" N   LEU A 253 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 296
      Proline residue:  A 289  - end of helix
      removed outlier: 3.622A  pdb=" N   VAL A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 338
      removed outlier: 3.739A  pdb=" N   TYR A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 355
      removed outlier: 4.501A  pdb=" N   LYS A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   CYS A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 11
      removed outlier: 3.691A  pdb=" N   THR B   8 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU B   9 " --> pdb=" O   GLN B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU B  45 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      Proline residue:  B  46  - end of helix
    Processing helix  chain 'B' and resid 73 through 87
    Processing helix  chain 'B' and resid 99 through 131
      removed outlier: 4.420A  pdb=" N   LEU B 103 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
      Proline residue:  B 110  - end of helix
      Proline residue:  B 123  - end of helix
    Processing helix  chain 'B' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 206
      removed outlier: 3.554A  pdb=" N   TYR B 199 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 236
      removed outlier: 3.649A  pdb=" N   THR B 220 " --> pdb=" O   CYS B 216 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU B 221 " --> pdb=" O   HIS B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 255
      removed outlier: 3.975A  pdb=" N   LEU B 253 " --> pdb=" O   SER B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 296
      Proline residue:  B 289  - end of helix
      removed outlier: 3.622A  pdb=" N   VAL B 292 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 338
      removed outlier: 3.739A  pdb=" N   TYR B 331 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 355
      removed outlier: 4.501A  pdb=" N   LYS B 346 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   CYS B 347 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 11
      removed outlier: 3.691A  pdb=" N   THR C   8 " --> pdb=" O   ALA C   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU C   9 " --> pdb=" O   GLN C   5 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU C  45 " --> pdb=" O   ILE C  41 " (cutoff:3.500A)
      Proline residue:  C  46  - end of helix
    Processing helix  chain 'C' and resid 73 through 87
    Processing helix  chain 'C' and resid 99 through 131
      removed outlier: 4.419A  pdb=" N   LEU C 103 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      Proline residue:  C 110  - end of helix
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE C 135 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 206
      removed outlier: 3.554A  pdb=" N   TYR C 199 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 236
      removed outlier: 3.648A  pdb=" N   THR C 220 " --> pdb=" O   CYS C 216 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU C 221 " --> pdb=" O   HIS C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 255
      removed outlier: 3.975A  pdb=" N   LEU C 253 " --> pdb=" O   SER C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 296
      Proline residue:  C 289  - end of helix
      removed outlier: 3.622A  pdb=" N   VAL C 292 " --> pdb=" O   ALA C 288 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE C 296 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 338
      removed outlier: 3.739A  pdb=" N   TYR C 331 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 355
      removed outlier: 4.501A  pdb=" N   LYS C 346 " --> pdb=" O   VAL C 342 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   CYS C 347 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 11
      removed outlier: 3.690A  pdb=" N   THR D   8 " --> pdb=" O   ALA D   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU D   9 " --> pdb=" O   GLN D   5 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU D  45 " --> pdb=" O   ILE D  41 " (cutoff:3.500A)
      Proline residue:  D  46  - end of helix
    Processing helix  chain 'D' and resid 73 through 87
    Processing helix  chain 'D' and resid 99 through 131
      removed outlier: 4.420A  pdb=" N   LEU D 103 " --> pdb=" O   GLY D  99 " (cutoff:3.500A)
      Proline residue:  D 110  - end of helix
      Proline residue:  D 123  - end of helix
    Processing helix  chain 'D' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE D 135 " --> pdb=" O   ALA D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 206
      removed outlier: 3.554A  pdb=" N   TYR D 199 " --> pdb=" O   ILE D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 236
      removed outlier: 3.649A  pdb=" N   THR D 220 " --> pdb=" O   CYS D 216 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LEU D 221 " --> pdb=" O   HIS D 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 255
      removed outlier: 3.975A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 296
      Proline residue:  D 289  - end of helix
      removed outlier: 3.623A  pdb=" N   VAL D 292 " --> pdb=" O   ALA D 288 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE D 296 " --> pdb=" O   VAL D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 338
      removed outlier: 3.739A  pdb=" N   TYR D 331 " --> pdb=" O   ASP D 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 342 through 355
      removed outlier: 4.501A  pdb=" N   LYS D 346 " --> pdb=" O   VAL D 342 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   CYS D 347 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 11
      removed outlier: 3.690A  pdb=" N   THR E   8 " --> pdb=" O   ALA E   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU E   9 " --> pdb=" O   GLN E   5 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU E  45 " --> pdb=" O   ILE E  41 " (cutoff:3.500A)
      Proline residue:  E  46  - end of helix
    Processing helix  chain 'E' and resid 73 through 87
    Processing helix  chain 'E' and resid 99 through 131
      removed outlier: 4.420A  pdb=" N   LEU E 103 " --> pdb=" O   GLY E  99 " (cutoff:3.500A)
      Proline residue:  E 110  - end of helix
      Proline residue:  E 123  - end of helix
    Processing helix  chain 'E' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE E 135 " --> pdb=" O   ALA E 131 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 206
      removed outlier: 3.555A  pdb=" N   TYR E 199 " --> pdb=" O   ILE E 195 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 236
      removed outlier: 3.649A  pdb=" N   THR E 220 " --> pdb=" O   CYS E 216 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU E 221 " --> pdb=" O   HIS E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 255
      removed outlier: 3.976A  pdb=" N   LEU E 253 " --> pdb=" O   SER E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 270 through 296
      Proline residue:  E 289  - end of helix
      removed outlier: 3.623A  pdb=" N   VAL E 292 " --> pdb=" O   ALA E 288 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE E 296 " --> pdb=" O   VAL E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 327 through 338
      removed outlier: 3.738A  pdb=" N   TYR E 331 " --> pdb=" O   ASP E 327 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 342 through 355
      removed outlier: 4.502A  pdb=" N   LYS E 346 " --> pdb=" O   VAL E 342 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   CYS E 347 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 11
      removed outlier: 3.691A  pdb=" N   THR F   8 " --> pdb=" O   ALA F   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU F   9 " --> pdb=" O   GLN F   5 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU F  45 " --> pdb=" O   ILE F  41 " (cutoff:3.500A)
      Proline residue:  F  46  - end of helix
    Processing helix  chain 'F' and resid 73 through 87
    Processing helix  chain 'F' and resid 99 through 131
      removed outlier: 4.419A  pdb=" N   LEU F 103 " --> pdb=" O   GLY F  99 " (cutoff:3.500A)
      Proline residue:  F 110  - end of helix
      Proline residue:  F 123  - end of helix
    Processing helix  chain 'F' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE F 135 " --> pdb=" O   ALA F 131 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 195 through 206
      removed outlier: 3.554A  pdb=" N   TYR F 199 " --> pdb=" O   ILE F 195 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 209 through 236
      removed outlier: 3.649A  pdb=" N   THR F 220 " --> pdb=" O   CYS F 216 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LEU F 221 " --> pdb=" O   HIS F 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 250 through 255
      removed outlier: 3.975A  pdb=" N   LEU F 253 " --> pdb=" O   SER F 250 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 270 through 296
      Proline residue:  F 289  - end of helix
      removed outlier: 3.622A  pdb=" N   VAL F 292 " --> pdb=" O   ALA F 288 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE F 296 " --> pdb=" O   VAL F 292 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 327 through 338
      removed outlier: 3.739A  pdb=" N   TYR F 331 " --> pdb=" O   ASP F 327 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 342 through 355
      removed outlier: 4.501A  pdb=" N   LYS F 346 " --> pdb=" O   VAL F 342 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   CYS F 347 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 3 through 11
      removed outlier: 3.691A  pdb=" N   THR G   8 " --> pdb=" O   ALA G   4 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU G   9 " --> pdb=" O   GLN G   5 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 54
      removed outlier: 3.633A  pdb=" N   LEU G  45 " --> pdb=" O   ILE G  41 " (cutoff:3.500A)
      Proline residue:  G  46  - end of helix
    Processing helix  chain 'G' and resid 73 through 87
    Processing helix  chain 'G' and resid 99 through 131
      removed outlier: 4.421A  pdb=" N   LEU G 103 " --> pdb=" O   GLY G  99 " (cutoff:3.500A)
      Proline residue:  G 110  - end of helix
      Proline residue:  G 123  - end of helix
    Processing helix  chain 'G' and resid 131 through 155
      removed outlier: 4.089A  pdb=" N   ILE G 135 " --> pdb=" O   ALA G 131 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 206
      removed outlier: 3.554A  pdb=" N   TYR G 199 " --> pdb=" O   ILE G 195 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 209 through 236
      removed outlier: 3.650A  pdb=" N   THR G 220 " --> pdb=" O   CYS G 216 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LEU G 221 " --> pdb=" O   HIS G 217 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 250 through 255
      removed outlier: 3.975A  pdb=" N   LEU G 253 " --> pdb=" O   SER G 250 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 270 through 296
      Proline residue:  G 289  - end of helix
      removed outlier: 3.623A  pdb=" N   VAL G 292 " --> pdb=" O   ALA G 288 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE G 296 " --> pdb=" O   VAL G 292 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 327 through 338
      removed outlier: 3.739A  pdb=" N   TYR G 331 " --> pdb=" O   ASP G 327 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 342 through 355
      removed outlier: 4.501A  pdb=" N   LYS G 346 " --> pdb=" O   VAL G 342 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   CYS G 347 " --> pdb=" O   LYS G 343 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66
      removed outlier: 3.770A  pdb=" N   SER A  65 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS A 266 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66
      removed outlier: 3.771A  pdb=" N   SER B  65 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS B 266 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66
      removed outlier: 3.769A  pdb=" N   SER C  65 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS C 266 " --> pdb=" O   SER C  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66
      removed outlier: 3.769A  pdb=" N   SER D  65 " --> pdb=" O   LYS D 266 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS D 266 " --> pdb=" O   SER D  65 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66
      removed outlier: 3.770A  pdb=" N   SER E  65 " --> pdb=" O   LYS E 266 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS E 266 " --> pdb=" O   SER E  65 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66
      removed outlier: 3.770A  pdb=" N   SER F  65 " --> pdb=" O   LYS F 266 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS F 266 " --> pdb=" O   SER F  65 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66
      removed outlier: 3.770A  pdb=" N   SER G  65 " --> pdb=" O   LYS G 266 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS G 266 " --> pdb=" O   SER G  65 " (cutoff:3.500A)

    938 hydrogen bonds defined for protein.
    2751 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: 4.46

  Time building geometry restraints manager: 4.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4615
        1.34 -     1.46: 3610
        1.46 -     1.58: 7483
        1.58 -     1.69: 0
        1.69 -     1.81: 91
  Bond restraints: 15799
  Sorted by residual:
  bond pdb=" C   LEU D  45 "
       pdb=" N   PRO D  46 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.018 1.36e-02 5.41e+03 1.83e+00
  bond pdb=" C   LEU C  45 "
       pdb=" N   PRO C  46 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.018 1.36e-02 5.41e+03 1.80e+00
  bond pdb=" C   LEU A  45 "
       pdb=" N   PRO A  46 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.36e-02 5.41e+03 1.75e+00
  bond pdb=" C   LEU E  45 "
       pdb=" N   PRO E  46 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.36e-02 5.41e+03 1.74e+00
  bond pdb=" C   LEU F  45 "
       pdb=" N   PRO F  46 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.36e-02 5.41e+03 1.73e+00
  ... (remaining 15794 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 20719
        1.47 -     2.95: 585
        2.95 -     4.42: 130
        4.42 -     5.90: 77
        5.90 -     7.37: 7
  Bond angle restraints: 21518
  Sorted by residual:
  angle pdb=" N   ILE F   3 "
        pdb=" CA  ILE F   3 "
        pdb=" C   ILE F   3 "
      ideal   model   delta    sigma   weight residual
     112.96  109.05    3.91 1.00e+00 1.00e+00 1.53e+01
  angle pdb=" N   LYS B 140 "
        pdb=" CA  LYS B 140 "
        pdb=" CB  LYS B 140 "
      ideal   model   delta    sigma   weight residual
     110.12  114.73   -4.61 1.47e+00 4.63e-01 9.82e+00
  angle pdb=" N   LYS D 140 "
        pdb=" CA  LYS D 140 "
        pdb=" CB  LYS D 140 "
      ideal   model   delta    sigma   weight residual
     110.12  114.72   -4.60 1.47e+00 4.63e-01 9.78e+00
  angle pdb=" N   LYS A 140 "
        pdb=" CA  LYS A 140 "
        pdb=" CB  LYS A 140 "
      ideal   model   delta    sigma   weight residual
     110.12  114.69   -4.57 1.47e+00 4.63e-01 9.67e+00
  angle pdb=" N   LYS G 140 "
        pdb=" CA  LYS G 140 "
        pdb=" CB  LYS G 140 "
      ideal   model   delta    sigma   weight residual
     110.12  114.69   -4.57 1.47e+00 4.63e-01 9.66e+00
  ... (remaining 21513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 8349
       15.98 -    31.96: 730
       31.96 -    47.94: 252
       47.94 -    63.92: 49
       63.92 -    79.90: 7
  Dihedral angle restraints: 9387
    sinusoidal: 3381
      harmonic: 6006
  Sorted by residual:
  dihedral pdb=" CA  GLU C 352 "
           pdb=" C   GLU C 352 "
           pdb=" N   ASN C 353 "
           pdb=" CA  ASN C 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.24   19.76     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  GLU G 352 "
           pdb=" C   GLU G 352 "
           pdb=" N   ASN G 353 "
           pdb=" CA  ASN G 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  GLU A 352 "
           pdb=" C   GLU A 352 "
           pdb=" N   ASN A 353 "
           pdb=" CA  ASN A 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 9384 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1773
       0.034 -    0.067: 637
       0.067 -    0.101: 184
       0.101 -    0.135: 52
       0.135 -    0.168: 7
  Chirality restraints: 2653
  Sorted by residual:
  chirality pdb=" CA  GLU D 352 "
            pdb=" N   GLU D 352 "
            pdb=" C   GLU D 352 "
            pdb=" CB  GLU D 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.07e-01
  chirality pdb=" CA  GLU B 352 "
            pdb=" N   GLU B 352 "
            pdb=" C   GLU B 352 "
            pdb=" CB  GLU B 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CA  GLU A 352 "
            pdb=" N   GLU A 352 "
            pdb=" C   GLU A 352 "
            pdb=" CB  GLU A 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.73e-01
  ... (remaining 2650 not shown)

  Planarity restraints: 2590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 123 "   -0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO B 124 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 123 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO E 124 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO E 124 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 124 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 123 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO C 124 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 124 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 124 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 2587 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 4097
        2.80 -     3.33: 15636
        3.33 -     3.85: 24909
        3.85 -     4.38: 26262
        4.38 -     4.90: 45522
  Nonbonded interactions: 116426
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  73 "
            pdb=" OE1 GLN G  76 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG  SER C  73 "
            pdb=" OE1 GLN C  76 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER D  73 "
            pdb=" OE1 GLN D  76 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER A  73 "
            pdb=" OE1 GLN A  76 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER E  73 "
            pdb=" OE1 GLN E  76 "
     model   vdw
     2.280 3.040
  ... (remaining 116421 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: 0.14
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

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:             1.720
  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:          0.500
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     31.080
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15806  Z= 0.139
  Angle     :  0.672   7.374  21532  Z= 0.352
  Chirality :  0.039   0.168   2653
  Planarity :  0.004   0.033   2590
  Dihedral  : 14.162  79.903   5432
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  0.12 %
    Favored  : 99.46 %
  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:  0.49 (0.20), residues: 1946
  helix:  1.30 (0.15), residues: 1351
  sheet:  None (None), residues: 0
  loop : -2.03 (0.23), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 104 
 HIS   0.001   0.001   HIS F 106 
 PHE   0.009   0.001   PHE F 116 
 TYR   0.019   0.001   TYR D 230 
 ARG   0.001   0.000   ARG F 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14877 (  938)
  hydrogen bonds       : angle       4.33482 ( 2751)
  SS BOND              : bond        0.00213 (    7)
  SS BOND              : angle       0.85728 (   14)
  covalent geometry    : bond        0.00272 (15799)
  covalent geometry    : angle       0.67197 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 259
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
REVERT: A  261 ASP cc_start: 0.7862 (m-30) cc_final: 0.7542 (m-30)
REVERT: B  261 ASP cc_start: 0.7780 (m-30) cc_final: 0.7575 (p0)
REVERT: C   37 MET cc_start: 0.6277 (tpp) cc_final: 0.5980 (tpp)
REVERT: C   75 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7127 (tpp-160)
REVERT: C  224 ILE cc_start: 0.7368 (mm) cc_final: 0.7157 (mt)
REVERT: D   75 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7140 (tpp-160)
REVERT: D  198 GLN cc_start: 0.7449 (mp-120) cc_final: 0.7197 (mp-120)
REVERT: E   75 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6872 (tpp-160)
REVERT: E  261 ASP cc_start: 0.7667 (m-30) cc_final: 0.7366 (m-30)
REVERT: F   75 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7113 (tpp-160)
REVERT: F  224 ILE cc_start: 0.7200 (mm) cc_final: 0.6989 (mt)
REVERT: F  261 ASP cc_start: 0.7898 (m-30) cc_final: 0.7524 (m-30)
REVERT: F  296 PHE cc_start: 0.7527 (m-10) cc_final: 0.7236 (m-10)
REVERT: G   75 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7197 (tpp-160)
REVERT: G  261 ASP cc_start: 0.7668 (m-30) cc_final: 0.7424 (p0)
  outliers start: 7
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2359
  time to fit residues: 93.4492
Evaluate side-chains
  222 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 217
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain D residue   75 ARG
Chi-restraints excluded: chain E residue   75 ARG
Chi-restraints excluded: chain F residue   75 ARG
Chi-restraints excluded: chain G residue   75 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    5.9990
   chunk 148 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 153 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9990
   chunk 114 optimal weight:    0.8980
   chunk 177 optimal weight:    1.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.180847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.133231 restraints weight = 20529.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137977 restraints weight = 12169.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.141104 restraints weight = 8693.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15806  Z= 0.139
  Angle     :  0.626   6.399  21532  Z= 0.312
  Chirality :  0.040   0.125   2653
  Planarity :  0.004   0.033   2590
  Dihedral  :  5.526  56.941   2120
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.92 %
    Favored  : 86.62 %
  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:  0.53 (0.20), residues: 1946
  helix:  1.30 (0.15), residues: 1400
  sheet:  None (None), residues: 0
  loop : -2.19 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 104 
 HIS   0.002   0.001   HIS G 217 
 PHE   0.013   0.001   PHE F 244 
 TYR   0.022   0.001   TYR D 121 
 ARG   0.001   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03733 (  938)
  hydrogen bonds       : angle       3.54202 ( 2751)
  SS BOND              : bond        0.00497 (    7)
  SS BOND              : angle       1.71617 (   14)
  covalent geometry    : bond        0.00324 (15799)
  covalent geometry    : angle       0.62431 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 1.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.5484 (tpp) cc_final: 0.5130 (tpp)
REVERT: A  261 ASP cc_start: 0.7867 (m-30) cc_final: 0.7566 (m-30)
REVERT: A  334 PHE cc_start: 0.7177 (m-10) cc_final: 0.6828 (m-80)
REVERT: B  334 PHE cc_start: 0.7128 (m-10) cc_final: 0.6722 (m-80)
REVERT: C   37 MET cc_start: 0.6335 (tpp) cc_final: 0.5924 (tpp)
REVERT: C   75 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7033 (tpp-160)
REVERT: C  224 ILE cc_start: 0.7295 (mm) cc_final: 0.7016 (mt)
REVERT: C  334 PHE cc_start: 0.7072 (m-10) cc_final: 0.6636 (m-80)
REVERT: D   75 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7021 (tpp-160)
REVERT: D  334 PHE cc_start: 0.6909 (m-10) cc_final: 0.6505 (m-80)
REVERT: E   75 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6889 (tpp-160)
REVERT: E  261 ASP cc_start: 0.7857 (m-30) cc_final: 0.7526 (m-30)
REVERT: E  334 PHE cc_start: 0.7010 (m-10) cc_final: 0.6624 (m-80)
REVERT: F  224 ILE cc_start: 0.7164 (mm) cc_final: 0.6938 (mt)
REVERT: F  334 PHE cc_start: 0.7191 (m-10) cc_final: 0.6924 (m-80)
REVERT: G   75 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7059 (tpp-160)
REVERT: G  261 ASP cc_start: 0.7826 (m-30) cc_final: 0.7521 (p0)
REVERT: G  334 PHE cc_start: 0.7035 (m-10) cc_final: 0.6821 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 240
  average time/residue: 0.2318
  time to fit residues: 86.1587
Evaluate side-chains
  235 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 212
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  347 CYS
Chi-restraints excluded: chain D residue   75 ARG
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue   75 ARG
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  347 CYS
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  347 CYS
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  129 PHE
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  347 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 170 optimal weight:    0.9990
   chunk 146 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 153 optimal weight:    5.9990
   chunk 181 optimal weight:    6.9990
   chunk 84 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 155 optimal weight:   10.0000
   chunk 45 optimal weight:    0.5980
   chunk 132 optimal weight:    4.9990
   chunk 168 optimal weight:    0.6980
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.181039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.133428 restraints weight = 20442.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138294 restraints weight = 12091.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.141540 restraints weight = 8598.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15806  Z= 0.122
  Angle     :  0.603   9.234  21532  Z= 0.292
  Chirality :  0.039   0.116   2653
  Planarity :  0.004   0.036   2590
  Dihedral  :  4.959  59.474   2116
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.80 %
    Favored  : 83.17 %
  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:  0.78 (0.20), residues: 1946
  helix:  1.54 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.99 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 104 
 HIS   0.002   0.001   HIS G 217 
 PHE   0.010   0.001   PHE F 244 
 TYR   0.024   0.002   TYR F 121 
 ARG   0.001   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  938)
  hydrogen bonds       : angle       3.35203 ( 2751)
  SS BOND              : bond        0.00339 (    7)
  SS BOND              : angle       1.38479 (   14)
  covalent geometry    : bond        0.00279 (15799)
  covalent geometry    : angle       0.60197 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 229
  time to evaluate  : 1.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.5501 (tpp) cc_final: 0.5210 (tpp)
REVERT: A  334 PHE cc_start: 0.7128 (m-10) cc_final: 0.6816 (m-80)
REVERT: B  334 PHE cc_start: 0.6952 (m-10) cc_final: 0.6538 (m-80)
REVERT: C   37 MET cc_start: 0.6141 (tpp) cc_final: 0.5586 (tpp)
REVERT: C   75 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6993 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7947 (mp-120) cc_final: 0.7342 (mp10)
REVERT: C  334 PHE cc_start: 0.6960 (m-10) cc_final: 0.6512 (m-80)
REVERT: D  147 ASP cc_start: 0.8099 (t70) cc_final: 0.7752 (t0)
REVERT: D  334 PHE cc_start: 0.6913 (m-10) cc_final: 0.6556 (m-80)
REVERT: E  334 PHE cc_start: 0.7031 (m-10) cc_final: 0.6677 (m-80)
REVERT: F  198 GLN cc_start: 0.7612 (mp-120) cc_final: 0.7074 (mp10)
REVERT: F  334 PHE cc_start: 0.7035 (m-10) cc_final: 0.6833 (m-80)
REVERT: G   75 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7033 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6975 (m-10) cc_final: 0.6741 (m-80)
  outliers start: 50
  outliers final: 32
  residues processed: 251
  average time/residue: 0.2340
  time to fit residues: 90.1816
Evaluate side-chains
  253 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 219
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  347 CYS
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  347 CYS
Chi-restraints excluded: chain E residue  352 GLU
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  347 CYS
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  129 PHE
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  347 CYS
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 179 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0970
   chunk 125 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 167 optimal weight:    9.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
C 198 GLN
G 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.182322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.134894 restraints weight = 20300.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.139796 restraints weight = 11961.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.143077 restraints weight = 8484.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15806  Z= 0.111
  Angle     :  0.607  10.058  21532  Z= 0.286
  Chirality :  0.039   0.125   2653
  Planarity :  0.004   0.038   2590
  Dihedral  :  4.220  59.673   2108
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.40 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.20), residues: 1946
  helix:  1.63 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.88 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 104 
 HIS   0.003   0.001   HIS C 217 
 PHE   0.009   0.001   PHE F 244 
 TYR   0.024   0.001   TYR F 121 
 ARG   0.002   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  938)
  hydrogen bonds       : angle       3.25357 ( 2751)
  SS BOND              : bond        0.00208 (    7)
  SS BOND              : angle       1.13585 (   14)
  covalent geometry    : bond        0.00242 (15799)
  covalent geometry    : angle       0.60674 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 228
  time to evaluate  : 1.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.5409 (tpp) cc_final: 0.5146 (tpp)
REVERT: A  334 PHE cc_start: 0.7078 (m-10) cc_final: 0.6803 (m-80)
REVERT: B  334 PHE cc_start: 0.6980 (m-10) cc_final: 0.6523 (m-80)
REVERT: C   37 MET cc_start: 0.6041 (tpp) cc_final: 0.5535 (tpp)
REVERT: C   75 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7025 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7895 (mp10) cc_final: 0.7303 (mp10)
REVERT: C  334 PHE cc_start: 0.6949 (m-10) cc_final: 0.6508 (m-80)
REVERT: D  147 ASP cc_start: 0.8092 (t70) cc_final: 0.7757 (t0)
REVERT: D  334 PHE cc_start: 0.6810 (m-10) cc_final: 0.6478 (m-80)
REVERT: E  334 PHE cc_start: 0.7008 (m-10) cc_final: 0.6655 (m-80)
REVERT: F  198 GLN cc_start: 0.7584 (mp-120) cc_final: 0.7139 (mp10)
REVERT: F  334 PHE cc_start: 0.7033 (m-10) cc_final: 0.6820 (m-80)
REVERT: G   75 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7109 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6891 (m-10) cc_final: 0.6657 (m-80)
  outliers start: 48
  outliers final: 41
  residues processed: 247
  average time/residue: 0.2218
  time to fit residues: 85.2030
Evaluate side-chains
  251 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 208
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  129 PHE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain E residue  352 GLU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  129 PHE
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  129 PHE
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 141 optimal weight:    0.3980
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 149 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 84 optimal weight:   10.0000
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.180216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132391 restraints weight = 20708.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.137261 restraints weight = 12229.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.140534 restraints weight = 8691.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15806  Z= 0.120
  Angle     :  0.613  11.038  21532  Z= 0.292
  Chirality :  0.039   0.115   2653
  Planarity :  0.004   0.040   2590
  Dihedral  :  4.113  59.109   2108
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 17.43 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.20), residues: 1946
  helix:  1.67 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.83 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 104 
 HIS   0.002   0.001   HIS G 134 
 PHE   0.011   0.001   PHE F 244 
 TYR   0.025   0.002   TYR F 121 
 ARG   0.001   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  938)
  hydrogen bonds       : angle       3.26699 ( 2751)
  SS BOND              : bond        0.00280 (    7)
  SS BOND              : angle       1.30310 (   14)
  covalent geometry    : bond        0.00273 (15799)
  covalent geometry    : angle       0.61184 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 215
  time to evaluate  : 1.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.5292 (tpp) cc_final: 0.5090 (tpp)
REVERT: B  334 PHE cc_start: 0.7058 (m-10) cc_final: 0.6645 (m-80)
REVERT: C   37 MET cc_start: 0.5827 (tpp) cc_final: 0.5322 (tpp)
REVERT: C   75 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7119 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7891 (mp10) cc_final: 0.7048 (mp10)
REVERT: C  334 PHE cc_start: 0.6921 (m-10) cc_final: 0.6525 (m-80)
REVERT: D  198 GLN cc_start: 0.7301 (mp-120) cc_final: 0.7001 (mp10)
REVERT: D  334 PHE cc_start: 0.6891 (m-10) cc_final: 0.6554 (m-80)
REVERT: E  334 PHE cc_start: 0.7116 (m-10) cc_final: 0.6765 (m-80)
REVERT: F  198 GLN cc_start: 0.7585 (mp-120) cc_final: 0.7002 (mp10)
REVERT: G   75 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7128 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6931 (m-10) cc_final: 0.6677 (m-80)
  outliers start: 50
  outliers final: 45
  residues processed: 237
  average time/residue: 0.2353
  time to fit residues: 86.0207
Evaluate side-chains
  254 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 207
  time to evaluate  : 1.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  347 CYS
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  129 PHE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain E residue  347 CYS
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  129 PHE
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  347 CYS
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    0.3980
   chunk 160 optimal weight:    0.6980
   chunk 141 optimal weight:    0.0000
   chunk 155 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0970
   chunk 164 optimal weight:    0.9980
   chunk 158 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.4182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.182964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.135211 restraints weight = 20601.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.140221 restraints weight = 12115.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.143510 restraints weight = 8568.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15806  Z= 0.107
  Angle     :  0.599   9.424  21532  Z= 0.284
  Chirality :  0.038   0.147   2653
  Planarity :  0.004   0.040   2590
  Dihedral  :  3.932  58.681   2108
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.52 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.20), residues: 1946
  helix:  1.74 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.74 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 104 
 HIS   0.003   0.001   HIS C 217 
 PHE   0.009   0.001   PHE F 334 
 TYR   0.025   0.001   TYR F 121 
 ARG   0.002   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02861 (  938)
  hydrogen bonds       : angle       3.16576 ( 2751)
  SS BOND              : bond        0.00156 (    7)
  SS BOND              : angle       1.05381 (   14)
  covalent geometry    : bond        0.00227 (15799)
  covalent geometry    : angle       0.59837 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 217
  time to evaluate  : 1.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  334 PHE cc_start: 0.6974 (m-10) cc_final: 0.6555 (m-80)
REVERT: C   37 MET cc_start: 0.5767 (tpp) cc_final: 0.5284 (tpp)
REVERT: C   75 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7077 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7860 (mp10) cc_final: 0.7430 (mm-40)
REVERT: C  334 PHE cc_start: 0.6753 (m-10) cc_final: 0.6384 (m-80)
REVERT: D  147 ASP cc_start: 0.8114 (t70) cc_final: 0.7782 (t0)
REVERT: D  334 PHE cc_start: 0.6855 (m-10) cc_final: 0.6524 (m-80)
REVERT: E  334 PHE cc_start: 0.6927 (m-10) cc_final: 0.6571 (m-80)
REVERT: F  198 GLN cc_start: 0.7561 (mp-120) cc_final: 0.7296 (mp10)
REVERT: G   75 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7131 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6768 (m-10) cc_final: 0.6496 (m-80)
  outliers start: 48
  outliers final: 43
  residues processed: 235
  average time/residue: 0.2465
  time to fit residues: 88.5749
Evaluate side-chains
  253 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 208
  time to evaluate  : 1.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  129 PHE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  115 LEU
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  129 PHE
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  347 CYS
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  129 PHE
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 111 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 151 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.180481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.132445 restraints weight = 20830.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.137401 restraints weight = 12309.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.140607 restraints weight = 8732.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15806  Z= 0.119
  Angle     :  0.607  10.964  21532  Z= 0.291
  Chirality :  0.039   0.129   2653
  Planarity :  0.004   0.040   2590
  Dihedral  :  3.998  58.400   2108
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.31 %
    Favored  : 77.48 %
  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:  1.05 (0.20), residues: 1946
  helix:  1.67 (0.15), residues: 1365
  sheet:  None (None), residues: 0
  loop : -1.73 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 104 
 HIS   0.002   0.001   HIS G 134 
 PHE   0.011   0.001   PHE A 244 
 TYR   0.026   0.002   TYR F 121 
 ARG   0.001   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03111 (  938)
  hydrogen bonds       : angle       3.23481 ( 2751)
  SS BOND              : bond        0.00258 (    7)
  SS BOND              : angle       1.16745 (   14)
  covalent geometry    : bond        0.00273 (15799)
  covalent geometry    : angle       0.60696 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 220
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  334 PHE cc_start: 0.7067 (m-10) cc_final: 0.6650 (m-80)
REVERT: C   37 MET cc_start: 0.5899 (tpp) cc_final: 0.5463 (tpp)
REVERT: C   75 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7117 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7900 (mp10) cc_final: 0.7463 (mm-40)
REVERT: C  334 PHE cc_start: 0.6922 (m-10) cc_final: 0.6532 (m-80)
REVERT: D  334 PHE cc_start: 0.6932 (m-10) cc_final: 0.6594 (m-80)
REVERT: E  334 PHE cc_start: 0.7129 (m-10) cc_final: 0.6776 (m-80)
REVERT: F  198 GLN cc_start: 0.7576 (mp-120) cc_final: 0.7003 (mp10)
REVERT: G   75 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7134 (tpp-160)
REVERT: G  201 LYS cc_start: 0.6785 (pttm) cc_final: 0.6556 (tptt)
REVERT: G  334 PHE cc_start: 0.6787 (m-10) cc_final: 0.6575 (m-80)
  outliers start: 53
  outliers final: 42
  residues processed: 247
  average time/residue: 0.2388
  time to fit residues: 90.0705
Evaluate side-chains
  254 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 210
  time to evaluate  : 1.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  347 CYS
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  115 LEU
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 163 optimal weight:    0.8980
   chunk 85 optimal weight:   20.0000
   chunk 126 optimal weight:    0.9990
   chunk 155 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 191 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 159 optimal weight:    0.0980
   chunk 169 optimal weight:    0.0670
   chunk 125 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.5518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.181501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.133702 restraints weight = 20573.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.138704 restraints weight = 12155.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.141922 restraints weight = 8601.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  15806  Z= 0.112
  Angle     :  0.609  11.585  21532  Z= 0.290
  Chirality :  0.038   0.121   2653
  Planarity :  0.004   0.041   2590
  Dihedral  :  3.927  58.379   2108
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.92 %
    Favored  : 77.06 %
  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:  1.08 (0.20), residues: 1946
  helix:  1.76 (0.15), residues: 1351
  sheet:  None (None), residues: 0
  loop : -1.81 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 104 
 HIS   0.002   0.001   HIS C 217 
 PHE   0.010   0.001   PHE C 244 
 TYR   0.026   0.001   TYR F 121 
 ARG   0.002   0.000   ARG F  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02934 (  938)
  hydrogen bonds       : angle       3.18691 ( 2751)
  SS BOND              : bond        0.00205 (    7)
  SS BOND              : angle       1.11772 (   14)
  covalent geometry    : bond        0.00249 (15799)
  covalent geometry    : angle       0.60813 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 218
  time to evaluate  : 1.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 GLN cc_start: 0.8433 (pm20) cc_final: 0.8189 (mt0)
REVERT: B  198 GLN cc_start: 0.7037 (mp10) cc_final: 0.6724 (mp10)
REVERT: B  199 TYR cc_start: 0.7392 (t80) cc_final: 0.6996 (t80)
REVERT: B  224 ILE cc_start: 0.7128 (mm) cc_final: 0.6921 (mt)
REVERT: B  334 PHE cc_start: 0.7053 (m-10) cc_final: 0.6678 (m-80)
REVERT: B  352 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7649 (pp20)
REVERT: C   37 MET cc_start: 0.5788 (tpp) cc_final: 0.5389 (tpp)
REVERT: C   75 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7088 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7825 (mp10) cc_final: 0.7376 (mm-40)
REVERT: C  224 ILE cc_start: 0.7194 (mm) cc_final: 0.6993 (mt)
REVERT: C  334 PHE cc_start: 0.6928 (m-10) cc_final: 0.6532 (m-80)
REVERT: D  334 PHE cc_start: 0.6928 (m-10) cc_final: 0.6598 (m-80)
REVERT: D  352 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7678 (pp20)
REVERT: E  334 PHE cc_start: 0.7127 (m-10) cc_final: 0.6777 (m-80)
REVERT: F  198 GLN cc_start: 0.7538 (mp-120) cc_final: 0.7067 (mp10)
REVERT: F  256 ASP cc_start: 0.6931 (t0) cc_final: 0.6682 (t0)
REVERT: G   75 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7092 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6808 (m-10) cc_final: 0.6533 (m-80)
  outliers start: 50
  outliers final: 44
  residues processed: 241
  average time/residue: 0.2694
  time to fit residues: 100.5130
Evaluate side-chains
  259 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 211
  time to evaluate  : 2.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  129 PHE
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  115 LEU
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain E residue  352 GLU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  347 CYS
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  129 PHE
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 138 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   chunk 161 optimal weight:    1.9990
   chunk 139 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
F 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.180777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132770 restraints weight = 20617.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.137654 restraints weight = 12322.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.140904 restraints weight = 8795.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15806  Z= 0.117
  Angle     :  0.615  11.746  21532  Z= 0.294
  Chirality :  0.039   0.115   2653
  Planarity :  0.004   0.041   2590
  Dihedral  :  3.956  58.168   2108
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.22 %
    Favored  : 76.82 %
  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:  1.08 (0.20), residues: 1946
  helix:  1.69 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.68 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 104 
 HIS   0.002   0.001   HIS G 134 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.027   0.001   TYR F 121 
 ARG   0.001   0.000   ARG F  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03040 (  938)
  hydrogen bonds       : angle       3.21336 ( 2751)
  SS BOND              : bond        0.00256 (    7)
  SS BOND              : angle       1.14719 (   14)
  covalent geometry    : bond        0.00265 (15799)
  covalent geometry    : angle       0.61467 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 213
  time to evaluate  : 1.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 GLN cc_start: 0.8436 (pm20) cc_final: 0.8211 (mt0)
REVERT: B  334 PHE cc_start: 0.7080 (m-10) cc_final: 0.6700 (m-80)
REVERT: B  352 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7672 (pp20)
REVERT: C   37 MET cc_start: 0.5937 (tpp) cc_final: 0.5515 (tpp)
REVERT: C   75 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7018 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7813 (mp10) cc_final: 0.7389 (mm-40)
REVERT: C  256 ASP cc_start: 0.7764 (t0) cc_final: 0.7360 (t0)
REVERT: C  334 PHE cc_start: 0.6919 (m-10) cc_final: 0.6538 (m-80)
REVERT: C  352 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7724 (pp20)
REVERT: D  334 PHE cc_start: 0.6959 (m-10) cc_final: 0.6626 (m-80)
REVERT: D  352 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7706 (pp20)
REVERT: E  334 PHE cc_start: 0.7183 (m-10) cc_final: 0.6834 (m-80)
REVERT: F  198 GLN cc_start: 0.7496 (mp10) cc_final: 0.7183 (mp10)
REVERT: F  256 ASP cc_start: 0.6935 (t0) cc_final: 0.6688 (t0)
REVERT: G   75 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7028 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6920 (m-10) cc_final: 0.6644 (m-80)
REVERT: G  352 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7696 (pp20)
  outliers start: 49
  outliers final: 42
  residues processed: 237
  average time/residue: 0.2329
  time to fit residues: 85.8366
Evaluate side-chains
  257 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 209
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue   75 ARG
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  347 CYS
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  115 LEU
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain E residue  352 GLU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  347 CYS
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   62 THR
Chi-restraints excluded: chain G residue   75 ARG
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 116 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0470
   chunk 41 optimal weight:    8.9990
   chunk 193 optimal weight:    9.9990
   chunk 142 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   overall best weight:    0.9882

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.202102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.174567 restraints weight = 18283.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.173781 restraints weight = 22783.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.174282 restraints weight = 20231.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15806  Z= 0.141
  Angle     :  0.651  11.996  21532  Z= 0.313
  Chirality :  0.040   0.123   2653
  Planarity :  0.004   0.044   2590
  Dihedral  :  4.163  58.316   2108
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.52 %
    Favored  : 76.51 %
  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: 1946
  helix:  1.64 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.76 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  74 
 HIS   0.003   0.001   HIS F 134 
 PHE   0.013   0.001   PHE C 244 
 TYR   0.026   0.002   TYR E 121 
 ARG   0.001   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  938)
  hydrogen bonds       : angle       3.36933 ( 2751)
  SS BOND              : bond        0.00365 (    7)
  SS BOND              : angle       1.32471 (   14)
  covalent geometry    : bond        0.00337 (15799)
  covalent geometry    : angle       0.65009 (21518)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 230
  time to evaluate  : 1.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 GLN cc_start: 0.8141 (pm20) cc_final: 0.7880 (mt0)
REVERT: B  199 TYR cc_start: 0.7315 (t80) cc_final: 0.6989 (t80)
REVERT: B  224 ILE cc_start: 0.7547 (mm) cc_final: 0.7236 (mt)
REVERT: B  334 PHE cc_start: 0.6539 (m-10) cc_final: 0.6332 (m-80)
REVERT: B  352 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6774 (pp20)
REVERT: C   37 MET cc_start: 0.5788 (tpp) cc_final: 0.5553 (tpp)
REVERT: C  198 GLN cc_start: 0.7708 (mp10) cc_final: 0.6871 (mp10)
REVERT: C  224 ILE cc_start: 0.7659 (mm) cc_final: 0.7354 (mt)
REVERT: C  334 PHE cc_start: 0.6564 (m-10) cc_final: 0.6343 (m-80)
REVERT: C  352 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6682 (pp20)
REVERT: D  334 PHE cc_start: 0.6664 (m-10) cc_final: 0.6413 (m-80)
REVERT: D  352 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6301 (pp20)
REVERT: F  198 GLN cc_start: 0.7208 (mp10) cc_final: 0.6891 (mp10)
REVERT: F  262 GLN cc_start: 0.8068 (pm20) cc_final: 0.7868 (mt0)
REVERT: G  352 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6785 (pp20)
  outliers start: 49
  outliers final: 39
  residues processed: 254
  average time/residue: 0.2322
  time to fit residues: 91.1880
Evaluate side-chains
  261 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 218
  time to evaluate  : 1.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  347 CYS
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  129 PHE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  347 CYS
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  347 CYS
Chi-restraints excluded: chain D residue  352 GLU
Chi-restraints excluded: chain E residue   62 THR
Chi-restraints excluded: chain E residue  115 LEU
Chi-restraints excluded: chain E residue  120 LEU
Chi-restraints excluded: chain E residue  278 VAL
Chi-restraints excluded: chain E residue  285 VAL
Chi-restraints excluded: chain E residue  294 THR
Chi-restraints excluded: chain E residue  336 GLU
Chi-restraints excluded: chain E residue  352 GLU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  120 LEU
Chi-restraints excluded: chain F residue  278 VAL
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain F residue  352 GLU
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  120 LEU
Chi-restraints excluded: chain G residue  278 VAL
Chi-restraints excluded: chain G residue  285 VAL
Chi-restraints excluded: chain G residue  294 THR
Chi-restraints excluded: chain G residue  352 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 176 optimal weight:    2.9990
   chunk 157 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0270
   chunk 115 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.5638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.205899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.178796 restraints weight = 17936.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.177908 restraints weight = 23060.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.178813 restraints weight = 20023.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15806  Z= 0.116
  Angle     :  0.647  12.713  21532  Z= 0.304
  Chirality :  0.039   0.118   2653
  Planarity :  0.004   0.041   2590
  Dihedral  :  3.559  15.173   2100
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.13 %
    Favored  : 76.15 %
  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:  1.04 (0.20), residues: 1946
  helix:  1.68 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.72 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 104 
 HIS   0.002   0.001   HIS G 134 
 PHE   0.011   0.001   PHE G 334 
 TYR   0.027   0.001   TYR F 121 
 ARG   0.002   0.000   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  938)
  hydrogen bonds       : angle       3.23147 ( 2751)
  SS BOND              : bond        0.00220 (    7)
  SS BOND              : angle       1.09198 (   14)
  covalent geometry    : bond        0.00260 (15799)
  covalent geometry    : angle       0.64697 (21518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4094.79 seconds
wall clock time: 73 minutes 12.38 seconds (4392.38 seconds total)