Starting phenix.real_space_refine
on Fri Jun 13 21:59:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gts_34266/06_2025/8gts_34266_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gts_34266/06_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_34266/06_2025/8gts_34266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gts_34266/06_2025/8gts_34266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gts_34266/06_2025/8gts_34266_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gts_34266/06_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-5710/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: 5.76, per 1000 atoms: 0.37
  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: 4.00
  Conformation dependent library (CDL) restraints added in 2.2 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: 1.30
  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: 3.84

  Time building geometry restraints manager: 4.61 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: 0.13
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     32.140
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.670
-------------------------------------------------------------------------------
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  : 1.686 
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: 0.2489
  time to fit residues: 99.0625
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  : 1.672 
-------------------------------------------------------------------------------
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 = 49)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.133233 restraints weight = 20529.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137989 restraints weight = 12172.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.141130 restraints weight = 8687.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
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  : 1.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.5483 (tpp) cc_final: 0.5131 (tpp)
REVERT: A  261 ASP cc_start: 0.7861 (m-30) cc_final: 0.7562 (m-30)
REVERT: A  334 PHE cc_start: 0.7177 (m-10) cc_final: 0.6828 (m-80)
REVERT: B  334 PHE cc_start: 0.7131 (m-10) cc_final: 0.6722 (m-80)
REVERT: C   37 MET cc_start: 0.6333 (tpp) cc_final: 0.5925 (tpp)
REVERT: C   75 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7035 (tpp-160)
REVERT: C  224 ILE cc_start: 0.7305 (mm) cc_final: 0.7023 (mt)
REVERT: C  334 PHE cc_start: 0.7070 (m-10) cc_final: 0.6635 (m-80)
REVERT: D   75 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7022 (tpp-160)
REVERT: D  334 PHE cc_start: 0.6909 (m-10) cc_final: 0.6504 (m-80)
REVERT: E   75 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6892 (tpp-160)
REVERT: E  261 ASP cc_start: 0.7849 (m-30) cc_final: 0.7521 (m-30)
REVERT: E  334 PHE cc_start: 0.7011 (m-10) cc_final: 0.6624 (m-80)
REVERT: F  224 ILE cc_start: 0.7176 (mm) cc_final: 0.6948 (mt)
REVERT: F  334 PHE cc_start: 0.7190 (m-10) cc_final: 0.6921 (m-80)
REVERT: G   75 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7062 (tpp-160)
REVERT: G  261 ASP cc_start: 0.7825 (m-30) cc_final: 0.7524 (p0)
REVERT: G  334 PHE cc_start: 0.7037 (m-10) cc_final: 0.6821 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 240
  average time/residue: 0.2413
  time to fit residues: 90.0273
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  : 1.778 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 153 optimal weight:    5.9990
   chunk 181 optimal weight:    6.9990
   chunk 84 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   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:    0.6380

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.181697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.134330 restraints weight = 20387.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139148 restraints weight = 12072.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142378 restraints weight = 8605.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15806  Z= 0.118
  Angle     :  0.596   9.139  21532  Z= 0.288
  Chirality :  0.039   0.116   2653
  Planarity :  0.004   0.036   2590
  Dihedral  :  4.941  58.664   2116
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.86 %
    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:  0.80 (0.20), residues: 1946
  helix:  1.55 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.98 (0.23), residues: 588

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03316 (  938)
  hydrogen bonds       : angle       3.32402 ( 2751)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       1.33506 (   14)
  covalent geometry    : bond        0.00267 (15799)
  covalent geometry    : angle       0.59534 (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
  280 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 231
  time to evaluate  : 1.758 
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: symmetry clash
   revert: symmetry clash
REVERT: A  261 ASP cc_start: 0.7889 (m-30) cc_final: 0.7572 (m-30)
REVERT: A  334 PHE cc_start: 0.7108 (m-10) cc_final: 0.6799 (m-80)
REVERT: B  334 PHE cc_start: 0.6931 (m-10) cc_final: 0.6523 (m-80)
REVERT: C   37 MET cc_start: 0.6140 (tpp) cc_final: 0.5593 (tpp)
REVERT: C   75 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6971 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7926 (mp-120) cc_final: 0.7572 (mp10)
REVERT: C  201 LYS cc_start: 0.7261 (pttm) cc_final: 0.7019 (pttm)
REVERT: C  334 PHE cc_start: 0.6984 (m-10) cc_final: 0.6536 (m-80)
REVERT: D  147 ASP cc_start: 0.8084 (t70) cc_final: 0.7737 (t0)
REVERT: D  334 PHE cc_start: 0.6836 (m-10) cc_final: 0.6437 (m-80)
REVERT: E   75 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6668 (mmm160)
REVERT: E  334 PHE cc_start: 0.7001 (m-10) cc_final: 0.6644 (m-80)
REVERT: G   75 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7011 (tpp-160)
REVERT: G  261 ASP cc_start: 0.7893 (m-30) cc_final: 0.7568 (p0)
REVERT: G  334 PHE cc_start: 0.6971 (m-10) cc_final: 0.6745 (m-80)
  outliers start: 49
  outliers final: 30
  residues processed: 252
  average time/residue: 0.2367
  time to fit residues: 91.7652
Evaluate side-chains
  252 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 219
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
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  278 VAL
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  352 GLU
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  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:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 179 optimal weight:    0.0060
   chunk 8 optimal weight:    0.2980
   chunk 125 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 118 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 167 optimal weight:    0.0170
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.3634

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.184226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.136949 restraints weight = 20224.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.141880 restraints weight = 11876.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.145186 restraints weight = 8412.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  15806  Z= 0.106
  Angle     :  0.600  10.046  21532  Z= 0.281
  Chirality :  0.038   0.126   2653
  Planarity :  0.004   0.037   2590
  Dihedral  :  4.433  59.962   2112
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.16 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.20), residues: 1946
  helix:  1.66 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.86 (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   0.010   0.001   PHE F 334 
 TYR   0.024   0.001   TYR F 121 
 ARG   0.002   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02909 (  938)
  hydrogen bonds       : angle       3.20056 ( 2751)
  SS BOND              : bond        0.00151 (    7)
  SS BOND              : angle       1.08721 (   14)
  covalent geometry    : bond        0.00222 (15799)
  covalent geometry    : angle       0.59926 (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
  274 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 226
  time to evaluate  : 1.738 
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: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6960 (m-10) cc_final: 0.6756 (m-80)
REVERT: B  334 PHE cc_start: 0.6906 (m-10) cc_final: 0.6455 (m-80)
REVERT: C   37 MET cc_start: 0.6031 (tpp) cc_final: 0.5520 (tpp)
REVERT: C   75 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6972 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7898 (mp-120) cc_final: 0.7442 (mp10)
REVERT: C  334 PHE cc_start: 0.6910 (m-10) cc_final: 0.6475 (m-80)
REVERT: D  147 ASP cc_start: 0.8072 (t70) cc_final: 0.7734 (t0)
REVERT: D  334 PHE cc_start: 0.6740 (m-10) cc_final: 0.6361 (m-80)
REVERT: E  334 PHE cc_start: 0.6817 (m-10) cc_final: 0.6479 (m-80)
REVERT: G   75 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7090 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6857 (m-10) cc_final: 0.6626 (m-80)
  outliers start: 48
  outliers final: 41
  residues processed: 246
  average time/residue: 0.2468
  time to fit residues: 92.9391
Evaluate side-chains
  249 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 206
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  129 PHE
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  347 CYS
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  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:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 141 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 149 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 8 optimal weight:    0.4980
   chunk 84 optimal weight:   10.0000
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.180944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133075 restraints weight = 20679.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138016 restraints weight = 12186.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.141274 restraints weight = 8622.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  15806  Z= 0.117
  Angle     :  0.604   8.199  21532  Z= 0.288
  Chirality :  0.039   0.116   2653
  Planarity :  0.004   0.039   2590
  Dihedral  :  4.102  59.561   2108
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.68 %
    Favored  : 79.48 %
  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:  1.00 (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 C 217 
 PHE   0.011   0.001   PHE E 244 
 TYR   0.024   0.002   TYR F 121 
 ARG   0.002   0.000   ARG F  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  938)
  hydrogen bonds       : angle       3.24103 ( 2751)
  SS BOND              : bond        0.00268 (    7)
  SS BOND              : angle       1.27885 (   14)
  covalent geometry    : bond        0.00264 (15799)
  covalent geometry    : angle       0.60320 (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
  269 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 222
  time to evaluate  : 1.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  334 PHE cc_start: 0.6954 (m-10) cc_final: 0.6533 (m-80)
REVERT: C   37 MET cc_start: 0.5844 (tpp) cc_final: 0.5366 (tpp)
REVERT: C   75 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7118 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7908 (mp-120) cc_final: 0.7165 (mp10)
REVERT: C  334 PHE cc_start: 0.6802 (m-10) cc_final: 0.6424 (m-80)
REVERT: D  198 GLN cc_start: 0.7299 (mp-120) cc_final: 0.7003 (mp10)
REVERT: D  334 PHE cc_start: 0.6876 (m-10) cc_final: 0.6537 (m-80)
REVERT: E  334 PHE cc_start: 0.6964 (m-10) cc_final: 0.6592 (m-80)
REVERT: G   75 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7149 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6920 (m-10) cc_final: 0.6660 (m-80)
  outliers start: 47
  outliers final: 41
  residues processed: 241
  average time/residue: 0.2428
  time to fit residues: 90.4548
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  : 1.722 
-------------------------------------------------------------------------------
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  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  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  347 CYS
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 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  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:    0.7980
   chunk 20 optimal weight:    0.0970
   chunk 160 optimal weight:    0.3980
   chunk 141 optimal weight:   20.0000
   chunk 155 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 119 optimal weight:    0.4980
   chunk 164 optimal weight:    3.9990
   chunk 158 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.182230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.134485 restraints weight = 20575.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139506 restraints weight = 12032.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.142794 restraints weight = 8491.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  15806  Z= 0.110
  Angle     :  0.605  12.181  21532  Z= 0.287
  Chirality :  0.038   0.140   2653
  Planarity :  0.004   0.039   2590
  Dihedral  :  3.962  59.261   2108
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.34 %
    Favored  : 78.75 %
  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:  1.71 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.73 (0.24), residues: 588

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   0.009   0.001   PHE C 244 
 TYR   0.025   0.001   TYR A 121 
 ARG   0.002   0.000   ARG F  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02957 (  938)
  hydrogen bonds       : angle       3.18958 ( 2751)
  SS BOND              : bond        0.00204 (    7)
  SS BOND              : angle       1.10842 (   14)
  covalent geometry    : bond        0.00243 (15799)
  covalent geometry    : angle       0.60419 (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
  266 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 218
  time to evaluate  : 1.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  334 PHE cc_start: 0.6961 (m-10) cc_final: 0.6547 (m-80)
REVERT: C   37 MET cc_start: 0.5608 (tpp) cc_final: 0.5113 (tpp)
REVERT: C   75 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7141 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7917 (mp-120) cc_final: 0.7130 (mp10)
REVERT: C  334 PHE cc_start: 0.6825 (m-10) cc_final: 0.6464 (m-80)
REVERT: D  147 ASP cc_start: 0.8096 (t70) cc_final: 0.7756 (t0)
REVERT: D  198 GLN cc_start: 0.7270 (mp-120) cc_final: 0.6953 (mp10)
REVERT: D  334 PHE cc_start: 0.6867 (m-10) cc_final: 0.6532 (m-80)
REVERT: E  334 PHE cc_start: 0.7038 (m-10) cc_final: 0.6670 (m-80)
REVERT: G   75 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7116 (tpp-160)
REVERT: G  334 PHE cc_start: 0.6781 (m-10) cc_final: 0.6504 (m-80)
  outliers start: 48
  outliers final: 45
  residues processed: 238
  average time/residue: 0.2525
  time to fit residues: 91.6719
Evaluate side-chains
  256 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 209
  time to evaluate  : 1.747 
-------------------------------------------------------------------------------
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   62 THR
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  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  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  347 CYS
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 151 optimal weight:    0.0980
   chunk 98 optimal weight:    3.9990
   chunk 71 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.181482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133273 restraints weight = 20790.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138241 restraints weight = 12386.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.141451 restraints weight = 8827.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.2207

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= 0.116
  Angle     :  0.611  11.785  21532  Z= 0.290
  Chirality :  0.038   0.127   2653
  Planarity :  0.004   0.040   2590
  Dihedral  :  3.974  58.635   2108
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.89 %
    Favored  : 77.72 %
  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:  1.71 (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   0.007   0.001   TRP C 104 
 HIS   0.002   0.001   HIS F 134 
 PHE   0.010   0.001   PHE E 244 
 TYR   0.025   0.001   TYR F 121 
 ARG   0.001   0.000   ARG F  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03048 (  938)
  hydrogen bonds       : angle       3.21300 ( 2751)
  SS BOND              : bond        0.00234 (    7)
  SS BOND              : angle       1.18875 (   14)
  covalent geometry    : bond        0.00263 (15799)
  covalent geometry    : angle       0.61070 (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
  274 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 218
  time to evaluate  : 1.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 GLN cc_start: 0.6792 (mp10) cc_final: 0.6552 (mp10)
REVERT: B  334 PHE cc_start: 0.7066 (m-10) cc_final: 0.6654 (m-80)
REVERT: C   37 MET cc_start: 0.5761 (tpp) cc_final: 0.5277 (tpp)
REVERT: C   75 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7107 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7664 (mp-120) cc_final: 0.7011 (mp10)
REVERT: C  334 PHE cc_start: 0.6957 (m-10) cc_final: 0.6568 (m-80)
REVERT: D  198 GLN cc_start: 0.7458 (mp-120) cc_final: 0.7054 (mp10)
REVERT: D  334 PHE cc_start: 0.6917 (m-10) cc_final: 0.6577 (m-80)
REVERT: E  334 PHE cc_start: 0.7120 (m-10) cc_final: 0.6769 (m-80)
REVERT: G  334 PHE cc_start: 0.6806 (m-10) cc_final: 0.6558 (m-80)
  outliers start: 56
  outliers final: 44
  residues processed: 245
  average time/residue: 0.2873
  time to fit residues: 108.2416
Evaluate side-chains
  256 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 211
  time to evaluate  : 1.782 
-------------------------------------------------------------------------------
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   62 THR
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  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  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  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:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 126 optimal weight:    5.9990
   chunk 155 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 191 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 159 optimal weight:    1.9990
   chunk 169 optimal weight:   20.0000
   chunk 125 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.174810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.126949 restraints weight = 20880.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.131581 restraints weight = 12536.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.134695 restraints weight = 9014.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  15806  Z= 0.172
  Angle     :  0.682  12.093  21532  Z= 0.333
  Chirality :  0.041   0.126   2653
  Planarity :  0.004   0.042   2590
  Dihedral  :  4.236  58.475   2104
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.46 %
    Favored  : 76.76 %
  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:  0.63 (0.20), residues: 1946
  helix:  1.30 (0.15), residues: 1407
  sheet:  None (None), residues: 0
  loop : -1.97 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  74 
 HIS   0.004   0.001   HIS F 134 
 PHE   0.014   0.001   PHE E 244 
 TYR   0.027   0.002   TYR F 121 
 ARG   0.003   0.000   ARG G  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  938)
  hydrogen bonds       : angle       3.55284 ( 2751)
  SS BOND              : bond        0.00474 (    7)
  SS BOND              : angle       1.51941 (   14)
  covalent geometry    : bond        0.00424 (15799)
  covalent geometry    : angle       0.68157 (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
  290 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 244
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.6826 (pttm) cc_final: 0.6600 (pttm)
REVERT: B  198 GLN cc_start: 0.7357 (mp10) cc_final: 0.7013 (mp10)
REVERT: B  334 PHE cc_start: 0.7167 (m-10) cc_final: 0.6793 (m-80)
REVERT: B  352 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (pp20)
REVERT: C   37 MET cc_start: 0.5644 (tpp) cc_final: 0.5153 (tpp)
REVERT: C   75 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7125 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7699 (mp-120) cc_final: 0.7036 (mp10)
REVERT: C  256 ASP cc_start: 0.7406 (t0) cc_final: 0.7095 (t0)
REVERT: C  262 GLN cc_start: 0.8421 (pm20) cc_final: 0.8091 (pm20)
REVERT: C  264 GLN cc_start: 0.8390 (tp40) cc_final: 0.8144 (tp40)
REVERT: C  334 PHE cc_start: 0.7148 (m-10) cc_final: 0.6724 (m-80)
REVERT: D  352 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7718 (pp20)
REVERT: E  334 PHE cc_start: 0.7375 (m-10) cc_final: 0.6961 (m-80)
REVERT: G  264 GLN cc_start: 0.8351 (tp40) cc_final: 0.8128 (tp40)
REVERT: G  334 PHE cc_start: 0.7142 (m-10) cc_final: 0.6912 (m-80)
  outliers start: 46
  outliers final: 38
  residues processed: 268
  average time/residue: 0.2431
  time to fit residues: 99.6546
Evaluate side-chains
  275 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 234
  time to evaluate  : 1.738 
-------------------------------------------------------------------------------
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   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  294 THR
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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 138 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 161 optimal weight:    0.0770
   chunk 139 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
G 205 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.181727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.133853 restraints weight = 20625.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138806 restraints weight = 12329.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.142092 restraints weight = 8797.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15806  Z= 0.114
  Angle     :  0.655  12.946  21532  Z= 0.304
  Chirality :  0.038   0.121   2653
  Planarity :  0.004   0.041   2590
  Dihedral  :  3.795  58.209   2104
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.25 %
    Favored  : 76.09 %
  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:  1.02 (0.20), residues: 1946
  helix:  1.67 (0.15), residues: 1358
  sheet:  None (None), residues: 0
  loop : -1.77 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 104 
 HIS   0.002   0.001   HIS D 134 
 PHE   0.015   0.001   PHE D 334 
 TYR   0.027   0.001   TYR F 121 
 ARG   0.002   0.000   ARG G  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  938)
  hydrogen bonds       : angle       3.22752 ( 2751)
  SS BOND              : bond        0.00143 (    7)
  SS BOND              : angle       1.08082 (   14)
  covalent geometry    : bond        0.00249 (15799)
  covalent geometry    : angle       0.65426 (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
  280 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 236
  time to evaluate  : 1.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 GLN cc_start: 0.8557 (pm20) cc_final: 0.8176 (mt0)
REVERT: B  262 GLN cc_start: 0.8391 (pm20) cc_final: 0.8170 (mt0)
REVERT: B  334 PHE cc_start: 0.7118 (m-10) cc_final: 0.6723 (m-80)
REVERT: B  352 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7674 (pp20)
REVERT: C   37 MET cc_start: 0.5657 (tpp) cc_final: 0.5269 (tpp)
REVERT: C   75 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7024 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7652 (mp-120) cc_final: 0.6983 (mp10)
REVERT: C  256 ASP cc_start: 0.7429 (t0) cc_final: 0.7081 (t0)
REVERT: C  334 PHE cc_start: 0.6946 (m-10) cc_final: 0.6577 (m-80)
REVERT: C  352 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7755 (pp20)
REVERT: D  352 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7680 (pp20)
REVERT: E  198 GLN cc_start: 0.7018 (mp10) cc_final: 0.6626 (mp10)
REVERT: E  334 PHE cc_start: 0.7204 (m-10) cc_final: 0.6843 (m-80)
REVERT: F  262 GLN cc_start: 0.8569 (pm20) cc_final: 0.8232 (mt0)
REVERT: G  334 PHE cc_start: 0.6917 (m-10) cc_final: 0.6645 (m-80)
REVERT: G  352 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7685 (pp20)
  outliers start: 44
  outliers final: 38
  residues processed: 256
  average time/residue: 0.2411
  time to fit residues: 95.5611
Evaluate side-chains
  273 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 230
  time to evaluate  : 1.761 
-------------------------------------------------------------------------------
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  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  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  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   43 VAL
Chi-restraints excluded: chain G residue   62 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 116 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0030
   chunk 41 optimal weight:    2.9990
   chunk 193 optimal weight:    0.3980
   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:    0.7980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
G  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.179492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.131485 restraints weight = 20946.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.136263 restraints weight = 12519.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139113 restraints weight = 8985.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15806  Z= 0.124
  Angle     :  0.669  13.671  21532  Z= 0.311
  Chirality :  0.039   0.116   2653
  Planarity :  0.004   0.042   2590
  Dihedral  :  3.805  58.111   2104
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.67 %
    Favored  : 75.67 %
  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:  1.02 (0.20), residues: 1946
  helix:  1.70 (0.15), residues: 1351
  sheet:  None (None), residues: 0
  loop : -1.82 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 104 
 HIS   0.002   0.001   HIS G 134 
 PHE   0.012   0.001   PHE C 244 
 TYR   0.028   0.002   TYR A 121 
 ARG   0.003   0.000   ARG G  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03116 (  938)
  hydrogen bonds       : angle       3.26786 ( 2751)
  SS BOND              : bond        0.00270 (    7)
  SS BOND              : angle       1.17376 (   14)
  covalent geometry    : bond        0.00287 (15799)
  covalent geometry    : angle       0.66844 (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
  274 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 230
  time to evaluate  : 1.676 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 GLN cc_start: 0.8497 (pm20) cc_final: 0.8224 (mt0)
REVERT: A  334 PHE cc_start: 0.6843 (m-80) cc_final: 0.6602 (m-80)
REVERT: B  334 PHE cc_start: 0.7076 (m-10) cc_final: 0.6700 (m-80)
REVERT: B  352 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7695 (pp20)
REVERT: C   37 MET cc_start: 0.5745 (tpp) cc_final: 0.5333 (tpp)
REVERT: C   75 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6998 (tpp-160)
REVERT: C  198 GLN cc_start: 0.7653 (mp-120) cc_final: 0.6985 (mp10)
REVERT: C  256 ASP cc_start: 0.7392 (t0) cc_final: 0.7044 (t0)
REVERT: C  334 PHE cc_start: 0.7017 (m-10) cc_final: 0.6632 (m-80)
REVERT: C  352 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7809 (pp20)
REVERT: D  352 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7341 (pp20)
REVERT: E  334 PHE cc_start: 0.7221 (m-10) cc_final: 0.6863 (m-80)
REVERT: F  352 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7889 (pp20)
REVERT: G  334 PHE cc_start: 0.6929 (m-10) cc_final: 0.6655 (m-80)
REVERT: G  352 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7707 (pp20)
  outliers start: 44
  outliers final: 38
  residues processed: 250
  average time/residue: 0.2493
  time to fit residues: 95.4996
Evaluate side-chains
  269 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 225
  time to evaluate  : 1.723 
-------------------------------------------------------------------------------
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  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  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   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:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 176 optimal weight:    0.7980
   chunk 157 optimal weight:    0.5980
   chunk 93 optimal weight:    0.7980
   chunk 57 optimal weight:   20.0000
   chunk 115 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
G  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.179207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.131212 restraints weight = 20813.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.135987 restraints weight = 12522.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.139168 restraints weight = 9006.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15806  Z= 0.125
  Angle     :  0.669  13.140  21532  Z= 0.312
  Chirality :  0.039   0.116   2653
  Planarity :  0.004   0.042   2590
  Dihedral  :  3.808  58.228   2104
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.31 %
    Favored  : 75.67 %
  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:  1.01 (0.20), residues: 1946
  helix:  1.70 (0.15), residues: 1351
  sheet:  None (None), residues: 0
  loop : -1.83 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 104 
 HIS   0.002   0.001   HIS G 134 
 PHE   0.012   0.001   PHE G 244 
 TYR   0.028   0.002   TYR A 121 
 ARG   0.003   0.000   ARG G  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03143 (  938)
  hydrogen bonds       : angle       3.26409 ( 2751)
  SS BOND              : bond        0.00300 (    7)
  SS BOND              : angle       1.21141 (   14)
  covalent geometry    : bond        0.00291 (15799)
  covalent geometry    : angle       0.66888 (21518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4527.76 seconds
wall clock time: 80 minutes 49.66 seconds (4849.66 seconds total)