Starting phenix.real_space_refine
on Tue Jul 29 06:58:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7x_36052/07_2025/8j7x_36052.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7x_36052/07_2025/8j7x_36052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j7x_36052/07_2025/8j7x_36052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7x_36052/07_2025/8j7x_36052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7x_36052/07_2025/8j7x_36052.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7x_36052/07_2025/8j7x_36052.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.054
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      48      5.16       5
     C    7122      2.51       5
     N    1860      2.21       5
     O    2106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11136
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2258
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 9, 'TRANS': 277}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1672
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203}
    Chain: "E"
      Number of atoms: 1638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1638
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    D, B, F
  Time building chain proxies: 7.75, per 1000 atoms: 0.70
  Number of scatterers: 11136
  At special positions: 0
  Unit cell: (79.06, 116.82, 162.84, 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      48     16.00
     O    2106      8.00
     N    1860      7.00
     C    7122      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 138 " - pdb=" SG  CYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 145 " - pdb=" SG  CYS E 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 145 " - pdb=" SG  CYS F 200 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.03
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 26 sheets defined
      33.8% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 32
      removed outlier: 4.253A  pdb=" N   PHE A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 57
    Processing helix  chain 'A' and resid 60 through 88
      removed outlier: 4.436A  pdb=" N   SER A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 131
    Processing helix  chain 'A' and resid 138 through 159
    Processing helix  chain 'A' and resid 231 through 260
      removed outlier: 3.522A  pdb=" N   GLN A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 294
      Proline residue:  A 284  - end of helix
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 4.321A  pdb=" N   ASN A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 314
    Processing helix  chain 'A' and resid 347 through 362
    Processing helix  chain 'C' and resid 83 through 87
      removed outlier: 3.873A  pdb=" N   ALA C  87 " --> pdb=" O   ALA C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 132
    Processing helix  chain 'C' and resid 187 through 193
      removed outlier: 3.713A  pdb=" N   HIS C 193 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.661A  pdb=" N   TYR E  32 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 3.955A  pdb=" N   THR E  90 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 161 through 163
      No H-bonds generated for 'chain 'E' and resid 161 through 163'
    Processing helix  chain 'F' and resid 28 through 32
      removed outlier: 3.660A  pdb=" N   TYR F  32 " --> pdb=" O   LEU F  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 90
      removed outlier: 3.955A  pdb=" N   THR F  90 " --> pdb=" O   ALA F  87 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 161 through 163
      No H-bonds generated for 'chain 'F' and resid 161 through 163'
    Processing helix  chain 'D' and resid 83 through 87
      removed outlier: 3.873A  pdb=" N   ALA D  87 " --> pdb=" O   ALA D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 132
    Processing helix  chain 'D' and resid 187 through 193
      removed outlier: 3.713A  pdb=" N   HIS D 193 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 32
    Processing helix  chain 'B' and resid 32 through 57
    Processing helix  chain 'B' and resid 60 through 88
      removed outlier: 4.436A  pdb=" N   SER B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 131
    Processing helix  chain 'B' and resid 138 through 159
    Processing helix  chain 'B' and resid 231 through 260
      removed outlier: 3.521A  pdb=" N   GLN B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 294
      Proline residue:  B 284  - end of helix
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 4.321A  pdb=" N   ASN B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 314
    Processing helix  chain 'B' and resid 347 through 362
    Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330
      removed outlier: 5.692A  pdb=" N   LEU A 321 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   GLU A 323 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS A 339 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   TYR A 334 " --> pdb=" O   GLN A 366 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   TYR A 368 " --> pdb=" O   TYR A 334 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   GLY A 336 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   GLN A 370 " --> pdb=" O   GLY A 336 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LEU A 338 " --> pdb=" O   GLN A 370 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   ASP A 372 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU A 340 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.719A  pdb=" N   MET C  37 " --> pdb=" O   TYR C  53 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   TYR C  53 " --> pdb=" O   MET C  37 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   TRP C  39 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13
      removed outlier: 3.804A  pdb=" N   THR C 101 " --> pdb=" O   GLN C  94 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122
      removed outlier: 3.768A  pdb=" N   ASN C 141 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   TYR C 177 " --> pdb=" O   ASN C 142 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158
      removed outlier: 3.732A  pdb=" N   ILE C 209 " --> pdb=" O   ALA C 200 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   HIS C 202 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   SER C 207 " --> pdb=" O   HIS C 202 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.541A  pdb=" N   THR E 112 " --> pdb=" O   TYR E  93 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR E  93 " --> pdb=" O   THR E 112 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL E  34 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   VAL E  50 " --> pdb=" O   VAL E  34 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.541A  pdb=" N   THR E 112 " --> pdb=" O   TYR E  93 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR E  93 " --> pdb=" O   THR E 112 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   TYR E 107 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129
      removed outlier: 3.506A  pdb=" N   GLY E 144 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR E 180 " --> pdb=" O   GLY E 149 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129
      removed outlier: 3.506A  pdb=" N   GLY E 144 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR E 180 " --> pdb=" O   GLY E 149 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159
    Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7
    Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12
      removed outlier: 3.541A  pdb=" N   THR F 112 " --> pdb=" O   TYR F  93 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR F  93 " --> pdb=" O   THR F 112 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL F  34 " --> pdb=" O   VAL F  50 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   VAL F  50 " --> pdb=" O   VAL F  34 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   TRP F  36 " --> pdb=" O   LEU F  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12
      removed outlier: 3.541A  pdb=" N   THR F 112 " --> pdb=" O   TYR F  93 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR F  93 " --> pdb=" O   THR F 112 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   TYR F 107 " --> pdb=" O   ARG F  97 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129
      removed outlier: 3.506A  pdb=" N   GLY F 144 " --> pdb=" O   LEU F 129 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR F 180 " --> pdb=" O   GLY F 149 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129
      removed outlier: 3.506A  pdb=" N   GLY F 144 " --> pdb=" O   LEU F 129 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR F 180 " --> pdb=" O   GLY F 149 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159
    Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7
    Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.720A  pdb=" N   MET D  37 " --> pdb=" O   TYR D  53 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   TYR D  53 " --> pdb=" O   MET D  37 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   TRP D  39 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.804A  pdb=" N   THR D 101 " --> pdb=" O   GLN D  94 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 30 through 31
    Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 122
      removed outlier: 3.767A  pdb=" N   ASN D 141 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   TYR D 177 " --> pdb=" O   ASN D 142 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 157 through 158
      removed outlier: 3.732A  pdb=" N   ILE D 209 " --> pdb=" O   ALA D 200 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   HIS D 202 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   SER D 207 " --> pdb=" O   HIS D 202 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 330
      removed outlier: 5.691A  pdb=" N   LEU B 321 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   GLU B 323 " --> pdb=" O   LYS B 339 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B 339 " --> pdb=" O   GLU B 323 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   TYR B 334 " --> pdb=" O   GLN B 366 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   TYR B 368 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLY B 336 " --> pdb=" O   TYR B 368 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   GLN B 370 " --> pdb=" O   GLY B 336 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LEU B 338 " --> pdb=" O   GLN B 370 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   ASP B 372 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU B 340 " --> pdb=" O   ASP B 372 " (cutoff:3.500A)

    662 hydrogen bonds defined for protein.
    1818 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: 3.86

  Time building geometry restraints manager: 3.54 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: 3553
        1.34 -     1.46: 2703
        1.46 -     1.58: 5078
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 11404
  Sorted by residual:
  bond pdb=" CG  PRO C  99 "
       pdb=" CD  PRO C  99 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.70e-02 1.37e+03 9.66e-01
  bond pdb=" CG  PRO D 145 "
       pdb=" CD  PRO D 145 "
    ideal  model  delta    sigma   weight residual
    1.512  1.486  0.026 2.70e-02 1.37e+03 9.50e-01
  bond pdb=" CG  PRO D  99 "
       pdb=" CD  PRO D  99 "
    ideal  model  delta    sigma   weight residual
    1.512  1.486  0.026 2.70e-02 1.37e+03 9.45e-01
  bond pdb=" CG  PRO C 145 "
       pdb=" CD  PRO C 145 "
    ideal  model  delta    sigma   weight residual
    1.512  1.486  0.026 2.70e-02 1.37e+03 9.22e-01
  bond pdb=" CG  PRO C  81 "
       pdb=" CD  PRO C  81 "
    ideal  model  delta    sigma   weight residual
    1.512  1.489  0.023 2.70e-02 1.37e+03 7.54e-01
  ... (remaining 11399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 15090
        1.07 -     2.15: 318
        2.15 -     3.22: 95
        3.22 -     4.30: 13
        4.30 -     5.37: 10
  Bond angle restraints: 15526
  Sorted by residual:
  angle pdb=" C   ARG C  54 "
        pdb=" N   ALA C  55 "
        pdb=" CA  ALA C  55 "
      ideal   model   delta    sigma   weight residual
     121.54  126.91   -5.37 1.91e+00 2.74e-01 7.91e+00
  angle pdb=" C   ARG D  54 "
        pdb=" N   ALA D  55 "
        pdb=" CA  ALA D  55 "
      ideal   model   delta    sigma   weight residual
     121.54  126.85   -5.31 1.91e+00 2.74e-01 7.74e+00
  angle pdb=" N   ALA C  55 "
        pdb=" CA  ALA C  55 "
        pdb=" C   ALA C  55 "
      ideal   model   delta    sigma   weight residual
     110.80  114.36   -3.56 2.13e+00 2.20e-01 2.79e+00
  angle pdb=" N   ASP A  94 "
        pdb=" CA  ASP A  94 "
        pdb=" CB  ASP A  94 "
      ideal   model   delta    sigma   weight residual
     113.65  111.21    2.44 1.47e+00 4.63e-01 2.75e+00
  angle pdb=" N   ALA D  55 "
        pdb=" CA  ALA D  55 "
        pdb=" C   ALA D  55 "
      ideal   model   delta    sigma   weight residual
     110.80  114.33   -3.53 2.13e+00 2.20e-01 2.74e+00
  ... (remaining 15521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6414
       17.98 -    35.96: 280
       35.96 -    53.94: 40
       53.94 -    71.92: 8
       71.92 -    89.90: 2
  Dihedral angle restraints: 6744
    sinusoidal: 2566
      harmonic: 4178
  Sorted by residual:
  dihedral pdb=" CB  CYS F 145 "
           pdb=" SG  CYS F 145 "
           pdb=" SG  CYS F 200 "
           pdb=" CB  CYS F 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  121.69  -28.69     1      1.00e+01 1.00e-02 1.18e+01
  dihedral pdb=" CB  CYS E 145 "
           pdb=" SG  CYS E 145 "
           pdb=" SG  CYS E 200 "
           pdb=" CB  CYS E 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  121.68  -28.68     1      1.00e+01 1.00e-02 1.18e+01
  dihedral pdb=" CA  ARG B 296 "
           pdb=" CB  ARG B 296 "
           pdb=" CG  ARG B 296 "
           pdb=" CD  ARG B 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.76  -54.24     3      1.50e+01 4.44e-03 9.27e+00
  ... (remaining 6741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1069
       0.028 -    0.055: 450
       0.055 -    0.083: 122
       0.083 -    0.110: 104
       0.110 -    0.138: 35
  Chirality restraints: 1780
  Sorted by residual:
  chirality pdb=" CA  ILE F  92 "
            pdb=" N   ILE F  92 "
            pdb=" C   ILE F  92 "
            pdb=" CB  ILE F  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE E  92 "
            pdb=" N   ILE E  92 "
            pdb=" C   ILE E  92 "
            pdb=" CB  ILE E  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CA  ILE D  52 "
            pdb=" N   ILE D  52 "
            pdb=" C   ILE D  52 "
            pdb=" CB  ILE D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 1777 not shown)

  Planarity restraints: 1966
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 188 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO F 189 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO F 189 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F 189 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 188 "    0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO E 189 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO E 189 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E 189 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP E 193 "   -0.016 5.00e-02 4.00e+02   2.40e-02 9.23e-01
        pdb=" N   PRO E 194 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO E 194 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 194 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 1963 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1070
        2.75 -     3.29: 10728
        3.29 -     3.83: 18446
        3.83 -     4.36: 21401
        4.36 -     4.90: 38584
  Nonbonded interactions: 90229
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 125 "
            pdb=" O   PRO E 128 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   PRO F 128 "
            pdb=" OG  SER D 125 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE1 GLU D 189 "
            pdb=" NH2 ARG D 192 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OE1 GLU C 189 "
            pdb=" NH2 ARG C 192 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" O   THR F 192 "
            pdb=" N   GLU F 196 "
     model   vdw
     2.302 3.120
  ... (remaining 90224 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.200
  Find NCS groups from input model:        0.210
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
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      :  0.002   0.035  11412  Z= 0.102
  Angle     :  0.448   5.371  15542  Z= 0.236
  Chirality :  0.040   0.138   1780
  Planarity :  0.003   0.041   1966
  Dihedral  : 10.166  89.901   4024
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.39 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.01 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.75 (0.23), residues: 1420
  helix:  3.14 (0.24), residues: 430
  sheet:  0.85 (0.25), residues: 462
  loop : -0.21 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 108 
 HIS   0.003   0.001   HIS B  70 
 PHE   0.015   0.001   PHE A 123 
 TYR   0.010   0.001   TYR E  94 
 ARG   0.003   0.000   ARG B 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17585 (  618)
  hydrogen bonds       : angle       7.13111 ( 1818)
  SS BOND              : bond        0.00123 (    8)
  SS BOND              : angle       0.39173 (   16)
  covalent geometry    : bond        0.00227 (11404)
  covalent geometry    : angle       0.44774 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 344
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ILE cc_start: 0.7857 (mm) cc_final: 0.7604 (mm)
REVERT: A  257 MET cc_start: 0.6632 (mmt) cc_final: 0.6334 (mmt)
REVERT: A  345 ASP cc_start: 0.6759 (p0) cc_final: 0.6453 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 346
  average time/residue: 0.2332
  time to fit residues: 113.4282
Evaluate side-chains
  213 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.0970
   chunk 106 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 109 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  70 HIS
C   6 GLN
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 128 GLN
C 214 ASN
E  73 ASN
E  86 GLN
E 160 ASN
D 128 GLN
D 161 ASN
B 137 HIS
B 232 GLN
B 354 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.087766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.063814 restraints weight = 25533.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.75
r_work: 0.2771 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  11412  Z= 0.180
  Angle     :  0.618   8.992  15542  Z= 0.320
  Chirality :  0.045   0.167   1780
  Planarity :  0.004   0.042   1966
  Dihedral  :  4.050  15.651   1538
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.17 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  :  9.02 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.45 (0.23), residues: 1420
  helix:  2.66 (0.23), residues: 430
  sheet:  0.90 (0.25), residues: 462
  loop : -0.41 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 159 
 HIS   0.006   0.001   HIS A  70 
 PHE   0.028   0.002   PHE A  73 
 TYR   0.026   0.002   TYR A 319 
 ARG   0.005   0.001   ARG D  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  618)
  hydrogen bonds       : angle       4.81692 ( 1818)
  SS BOND              : bond        0.00678 (    8)
  SS BOND              : angle       1.69258 (   16)
  covalent geometry    : bond        0.00415 (11404)
  covalent geometry    : angle       0.61597 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 230
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8509 (tptt) cc_final: 0.8179 (tppt)
REVERT: A   70 HIS cc_start: 0.7969 (t70) cc_final: 0.7761 (t70)
REVERT: A   71 MET cc_start: 0.9000 (mmp) cc_final: 0.8730 (mmp)
REVERT: A   72 PHE cc_start: 0.8518 (m-80) cc_final: 0.8270 (m-80)
REVERT: A  120 PHE cc_start: 0.8540 (t80) cc_final: 0.8305 (t80)
REVERT: A  153 LEU cc_start: 0.8173 (tp) cc_final: 0.7959 (mm)
REVERT: A  242 LEU cc_start: 0.9530 (tt) cc_final: 0.9127 (mt)
REVERT: A  257 MET cc_start: 0.6995 (mmt) cc_final: 0.6696 (mmt)
REVERT: A  264 MET cc_start: 0.7304 (pmm) cc_final: 0.6841 (mpp)
REVERT: A  345 ASP cc_start: 0.8870 (p0) cc_final: 0.8513 (p0)
REVERT: C    5 THR cc_start: 0.9047 (m) cc_final: 0.8835 (p)
REVERT: C   46 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8084 (mp10)
REVERT: C   83 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7987 (mt-10)
REVERT: C  158 GLU cc_start: 0.8664 (tp30) cc_final: 0.8411 (tp30)
REVERT: C  179 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7628 (tpt)
REVERT: F   82 MET cc_start: 0.9123 (ttp) cc_final: 0.8909 (ttp)
REVERT: F  176 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7803 (pm20)
REVERT: D   83 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: D  161 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8959 (p0)
REVERT: D  179 MET cc_start: 0.8420 (ttt) cc_final: 0.7879 (ttt)
REVERT: B   33 LYS cc_start: 0.8447 (tptp) cc_final: 0.7872 (tppt)
REVERT: B   71 MET cc_start: 0.9148 (mmm) cc_final: 0.8707 (mmp)
REVERT: B  294 MET cc_start: 0.9156 (mmm) cc_final: 0.8842 (mmt)
  outliers start: 37
  outliers final: 22
  residues processed: 245
  average time/residue: 0.2179
  time to fit residues: 76.7185
Evaluate side-chains
  226 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  179 MET
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  143 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain F residue  176 GLN
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  137 HIS
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  283 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 21 optimal weight:    0.0980
   chunk 108 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 139 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 ASN
F  73 ASN
B 137 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.086076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.062192 restraints weight = 26078.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 2.75
r_work: 0.2741 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11412  Z= 0.178
  Angle     :  0.570  10.998  15542  Z= 0.294
  Chirality :  0.043   0.153   1780
  Planarity :  0.004   0.047   1966
  Dihedral  :  3.976  15.226   1538
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.27 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.43 (0.22), residues: 1420
  helix:  2.69 (0.23), residues: 430
  sheet:  0.86 (0.25), residues: 462
  loop : -0.43 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 159 
 HIS   0.018   0.001   HIS B 137 
 PHE   0.026   0.002   PHE A  73 
 TYR   0.017   0.001   TYR C  53 
 ARG   0.008   0.001   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  618)
  hydrogen bonds       : angle       4.45410 ( 1818)
  SS BOND              : bond        0.00447 (    8)
  SS BOND              : angle       1.29041 (   16)
  covalent geometry    : bond        0.00411 (11404)
  covalent geometry    : angle       0.56909 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 214
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.8478 (t0) cc_final: 0.8166 (t0)
REVERT: A   71 MET cc_start: 0.9011 (mmp) cc_final: 0.8751 (mmp)
REVERT: A   72 PHE cc_start: 0.8569 (m-80) cc_final: 0.8304 (m-80)
REVERT: A   74 ASP cc_start: 0.8812 (m-30) cc_final: 0.8430 (m-30)
REVERT: A  120 PHE cc_start: 0.8637 (t80) cc_final: 0.8420 (t80)
REVERT: A  153 LEU cc_start: 0.8118 (tp) cc_final: 0.7912 (mm)
REVERT: A  257 MET cc_start: 0.6809 (mmt) cc_final: 0.6546 (mmt)
REVERT: A  288 GLU cc_start: 0.8640 (tt0) cc_final: 0.8313 (tt0)
REVERT: A  345 ASP cc_start: 0.9159 (p0) cc_final: 0.8908 (p0)
REVERT: C   46 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8321 (mp10)
REVERT: C   83 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7975 (mt-10)
REVERT: C  158 GLU cc_start: 0.8591 (tp30) cc_final: 0.8177 (tp30)
REVERT: C  179 MET cc_start: 0.8560 (tpt) cc_final: 0.7533 (tpt)
REVERT: E   85 LEU cc_start: 0.9175 (mm) cc_final: 0.8910 (mm)
REVERT: F    3 GLN cc_start: 0.8110 (mp10) cc_final: 0.7732 (mp10)
REVERT: F   43 LYS cc_start: 0.9113 (mttp) cc_final: 0.8853 (mtpp)
REVERT: F   72 ASP cc_start: 0.8241 (t0) cc_final: 0.7954 (t0)
REVERT: F  176 GLN cc_start: 0.8083 (pt0) cc_final: 0.7803 (pm20)
REVERT: F  178 ASP cc_start: 0.8611 (t70) cc_final: 0.7957 (t70)
REVERT: D   83 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: D  160 GLN cc_start: 0.8551 (pm20) cc_final: 0.8283 (mp10)
REVERT: D  161 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8779 (p0)
REVERT: D  179 MET cc_start: 0.8386 (ttt) cc_final: 0.7846 (ttt)
REVERT: B   33 LYS cc_start: 0.8441 (tptp) cc_final: 0.7836 (tppt)
REVERT: B   37 ASN cc_start: 0.9270 (m-40) cc_final: 0.8907 (m-40)
REVERT: B   71 MET cc_start: 0.9214 (mmm) cc_final: 0.8797 (mmp)
REVERT: B  319 TYR cc_start: 0.9061 (m-10) cc_final: 0.8828 (m-10)
  outliers start: 37
  outliers final: 27
  residues processed: 229
  average time/residue: 0.2306
  time to fit residues: 77.8936
Evaluate side-chains
  226 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 197
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  121 PHE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  137 HIS
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  290 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 131 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  37 ASN
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN
C 214 ASN
F 160 ASN
D   6 GLN
D 161 ASN
B 137 HIS
B 232 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.084754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.060645 restraints weight = 25938.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 2.74
r_work: 0.2711 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11412  Z= 0.211
  Angle     :  0.592  10.178  15542  Z= 0.306
  Chirality :  0.043   0.153   1780
  Planarity :  0.004   0.043   1966
  Dihedral  :  4.061  15.754   1538
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 12.48 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.38 (0.22), residues: 1420
  helix:  2.69 (0.23), residues: 430
  sheet:  0.79 (0.24), residues: 460
  loop : -0.44 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 108 
 HIS   0.021   0.002   HIS B 137 
 PHE   0.024   0.002   PHE A 117 
 TYR   0.016   0.001   TYR C  53 
 ARG   0.006   0.001   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03248 (  618)
  hydrogen bonds       : angle       4.34238 ( 1818)
  SS BOND              : bond        0.00425 (    8)
  SS BOND              : angle       1.13571 (   16)
  covalent geometry    : bond        0.00487 (11404)
  covalent geometry    : angle       0.59084 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 199
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8146 (tppt) cc_final: 0.7888 (tppt)
REVERT: A   71 MET cc_start: 0.8995 (mmp) cc_final: 0.8786 (mmp)
REVERT: A   72 PHE cc_start: 0.8735 (m-80) cc_final: 0.8411 (m-80)
REVERT: A  120 PHE cc_start: 0.8640 (t80) cc_final: 0.8439 (t80)
REVERT: A  153 LEU cc_start: 0.8100 (tp) cc_final: 0.7881 (mm)
REVERT: A  156 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8357 (mm)
REVERT: A  242 LEU cc_start: 0.9507 (tt) cc_final: 0.9013 (mt)
REVERT: A  257 MET cc_start: 0.6908 (mmt) cc_final: 0.6544 (mmt)
REVERT: A  258 MET cc_start: 0.8079 (mmm) cc_final: 0.7653 (mmm)
REVERT: A  264 MET cc_start: 0.7577 (pmm) cc_final: 0.6510 (mmp)
REVERT: A  345 ASP cc_start: 0.9317 (p0) cc_final: 0.8981 (p0)
REVERT: C   46 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8480 (mp10)
REVERT: C   83 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7993 (mt-10)
REVERT: C  158 GLU cc_start: 0.8652 (tp30) cc_final: 0.8222 (tp30)
REVERT: C  179 MET cc_start: 0.8809 (tpt) cc_final: 0.7665 (tpt)
REVERT: E    1 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: E   85 LEU cc_start: 0.9281 (mm) cc_final: 0.9005 (mm)
REVERT: F   16 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8748 (mm-40)
REVERT: F   43 LYS cc_start: 0.9255 (mttp) cc_final: 0.9006 (mtpp)
REVERT: F   72 ASP cc_start: 0.8357 (t0) cc_final: 0.8045 (t0)
REVERT: F   82 MET cc_start: 0.9272 (ttp) cc_final: 0.9044 (ttp)
REVERT: F  176 GLN cc_start: 0.8191 (pt0) cc_final: 0.7976 (pm20)
REVERT: F  178 ASP cc_start: 0.8662 (t70) cc_final: 0.8045 (t70)
REVERT: F  212 ASP cc_start: 0.9123 (m-30) cc_final: 0.8913 (m-30)
REVERT: D   83 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8165 (mt-10)
REVERT: D  154 ILE cc_start: 0.7867 (mm) cc_final: 0.7656 (mt)
REVERT: D  179 MET cc_start: 0.8391 (ttt) cc_final: 0.7941 (ttt)
REVERT: B   33 LYS cc_start: 0.8399 (tptp) cc_final: 0.8198 (tptp)
REVERT: B   71 MET cc_start: 0.9215 (mmm) cc_final: 0.8875 (mmp)
REVERT: B  323 GLU cc_start: 0.8474 (tt0) cc_final: 0.8246 (tt0)
  outliers start: 46
  outliers final: 29
  residues processed: 226
  average time/residue: 0.2065
  time to fit residues: 68.8232
Evaluate side-chains
  222 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  121 PHE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  137 HIS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  290 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 139 optimal weight:    2.9990
   chunk 132 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 ASN
D 160 GLN
B 137 HIS
B 232 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.083586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.059487 restraints weight = 26296.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.75
r_work: 0.2685 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11412  Z= 0.228
  Angle     :  0.585   8.339  15542  Z= 0.303
  Chirality :  0.044   0.177   1780
  Planarity :  0.004   0.042   1966
  Dihedral  :  4.098  17.025   1538
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 12.72 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.33 (0.22), residues: 1420
  helix:  2.73 (0.23), residues: 430
  sheet:  0.70 (0.24), residues: 460
  loop : -0.49 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 108 
 HIS   0.011   0.001   HIS A  70 
 PHE   0.023   0.002   PHE A 117 
 TYR   0.015   0.001   TYR C  53 
 ARG   0.009   0.000   ARG D  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  618)
  hydrogen bonds       : angle       4.32167 ( 1818)
  SS BOND              : bond        0.00374 (    8)
  SS BOND              : angle       1.10981 (   16)
  covalent geometry    : bond        0.00528 (11404)
  covalent geometry    : angle       0.58408 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 191
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.8439 (t0) cc_final: 0.8150 (t0)
REVERT: A   74 ASP cc_start: 0.8683 (m-30) cc_final: 0.8254 (m-30)
REVERT: A  156 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8319 (mm)
REVERT: A  258 MET cc_start: 0.8002 (mmm) cc_final: 0.7673 (mmm)
REVERT: A  345 ASP cc_start: 0.9333 (p0) cc_final: 0.8777 (p0)
REVERT: A  347 ASP cc_start: 0.8751 (t0) cc_final: 0.8516 (t0)
REVERT: C   46 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8472 (mp10)
REVERT: C   83 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7959 (mt-10)
REVERT: C  158 GLU cc_start: 0.8616 (tp30) cc_final: 0.8204 (tp30)
REVERT: E    1 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: F   43 LYS cc_start: 0.9296 (mttp) cc_final: 0.9076 (mtpp)
REVERT: F  176 GLN cc_start: 0.8264 (pt0) cc_final: 0.8042 (pm20)
REVERT: F  178 ASP cc_start: 0.8819 (t70) cc_final: 0.8257 (t70)
REVERT: F  212 ASP cc_start: 0.9181 (m-30) cc_final: 0.8876 (m-30)
REVERT: D   78 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9034 (t)
REVERT: D   83 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: D  154 ILE cc_start: 0.7997 (mm) cc_final: 0.7784 (mt)
REVERT: D  161 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8934 (p0)
REVERT: D  179 MET cc_start: 0.8497 (ttt) cc_final: 0.8084 (ttt)
REVERT: B  244 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7954 (m-30)
REVERT: B  264 MET cc_start: 0.6646 (mmp) cc_final: 0.6333 (mmm)
REVERT: B  323 GLU cc_start: 0.8510 (tt0) cc_final: 0.8210 (tt0)
  outliers start: 53
  outliers final: 30
  residues processed: 227
  average time/residue: 0.1997
  time to fit residues: 67.4848
Evaluate side-chains
  214 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 179
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  137 HIS
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  290 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 101 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 ASN
B 137 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.082600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.058511 restraints weight = 26386.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.73
r_work: 0.2664 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.5545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  11412  Z= 0.242
  Angle     :  0.602   8.983  15542  Z= 0.309
  Chirality :  0.044   0.268   1780
  Planarity :  0.004   0.040   1966
  Dihedral  :  4.164  16.559   1538
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 14.17 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.18 (0.22), residues: 1420
  helix:  2.50 (0.23), residues: 436
  sheet:  0.67 (0.24), residues: 460
  loop : -0.58 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 167 
 HIS   0.008   0.001   HIS B 137 
 PHE   0.026   0.002   PHE A 117 
 TYR   0.014   0.001   TYR C  53 
 ARG   0.004   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  618)
  hydrogen bonds       : angle       4.36408 ( 1818)
  SS BOND              : bond        0.00401 (    8)
  SS BOND              : angle       1.10891 (   16)
  covalent geometry    : bond        0.00565 (11404)
  covalent geometry    : angle       0.60087 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 184
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8342 (mm)
REVERT: A  258 MET cc_start: 0.7765 (mmm) cc_final: 0.7505 (mmm)
REVERT: A  288 GLU cc_start: 0.8844 (tt0) cc_final: 0.8628 (tt0)
REVERT: A  345 ASP cc_start: 0.9341 (p0) cc_final: 0.8799 (p0)
REVERT: C   46 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8476 (mp10)
REVERT: C   83 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7907 (mt-10)
REVERT: C  158 GLU cc_start: 0.8647 (tp30) cc_final: 0.8269 (tp30)
REVERT: E    1 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: E  212 ASP cc_start: 0.9068 (m-30) cc_final: 0.8812 (m-30)
REVERT: F   43 LYS cc_start: 0.9251 (mttp) cc_final: 0.9043 (mtpp)
REVERT: F  176 GLN cc_start: 0.8386 (pt0) cc_final: 0.8100 (pm20)
REVERT: F  178 ASP cc_start: 0.8840 (t70) cc_final: 0.8297 (t70)
REVERT: F  212 ASP cc_start: 0.9158 (m-30) cc_final: 0.8871 (m-30)
REVERT: D   83 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: D  161 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.9036 (p0)
REVERT: D  179 MET cc_start: 0.8571 (ttt) cc_final: 0.8158 (ttt)
REVERT: B   50 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8662 (m-80)
REVERT: B   71 MET cc_start: 0.9328 (mmm) cc_final: 0.8995 (mmp)
REVERT: B  264 MET cc_start: 0.6741 (mmp) cc_final: 0.6433 (mmm)
REVERT: B  323 GLU cc_start: 0.8544 (tt0) cc_final: 0.8254 (tt0)
  outliers start: 49
  outliers final: 35
  residues processed: 216
  average time/residue: 0.2228
  time to fit residues: 71.4942
Evaluate side-chains
  221 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 182
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  161 ASN
Chi-restraints excluded: chain D residue  164 LEU
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  137 HIS
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  270 CYS
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  290 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 232 GLN
C 214 ASN
B 137 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.084071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.060306 restraints weight = 26292.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.72
r_work: 0.2702 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.5641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11412  Z= 0.135
  Angle     :  0.592  14.885  15542  Z= 0.295
  Chirality :  0.043   0.281   1780
  Planarity :  0.004   0.038   1966
  Dihedral  :  3.979  16.841   1538
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.02 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.29 (0.22), residues: 1420
  helix:  2.63 (0.23), residues: 436
  sheet:  0.75 (0.24), residues: 462
  loop : -0.57 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 167 
 HIS   0.010   0.001   HIS B 137 
 PHE   0.026   0.001   PHE B 120 
 TYR   0.017   0.001   TYR E  32 
 ARG   0.003   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03206 (  618)
  hydrogen bonds       : angle       4.20557 ( 1818)
  SS BOND              : bond        0.00290 (    8)
  SS BOND              : angle       0.96613 (   16)
  covalent geometry    : bond        0.00315 (11404)
  covalent geometry    : angle       0.59144 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 193
  time to evaluate  : 1.258 
Fit side-chains
REVERT: A  156 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8163 (mm)
REVERT: A  258 MET cc_start: 0.7886 (mmm) cc_final: 0.7674 (mmm)
REVERT: A  288 GLU cc_start: 0.8793 (tt0) cc_final: 0.8553 (tt0)
REVERT: A  345 ASP cc_start: 0.9288 (p0) cc_final: 0.8718 (p0)
REVERT: C   46 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8433 (mp10)
REVERT: C   83 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: C  158 GLU cc_start: 0.8645 (tp30) cc_final: 0.8193 (tp30)
REVERT: C  179 MET cc_start: 0.8932 (tpp) cc_final: 0.8042 (tpp)
REVERT: E    1 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7903 (tm-30)
REVERT: F  176 GLN cc_start: 0.8360 (pt0) cc_final: 0.8110 (pm20)
REVERT: F  178 ASP cc_start: 0.8820 (t70) cc_final: 0.8298 (t70)
REVERT: F  212 ASP cc_start: 0.9133 (m-30) cc_final: 0.8858 (m-30)
REVERT: D   83 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8237 (mt-10)
REVERT: D  179 MET cc_start: 0.8475 (ttt) cc_final: 0.8112 (ttt)
REVERT: B   33 LYS cc_start: 0.8374 (tptp) cc_final: 0.7986 (tppt)
REVERT: B   50 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8604 (m-80)
REVERT: B  264 MET cc_start: 0.6466 (mmp) cc_final: 0.6160 (mmm)
REVERT: B  323 GLU cc_start: 0.8493 (tt0) cc_final: 0.8260 (tt0)
REVERT: B  347 ASP cc_start: 0.8821 (t0) cc_final: 0.8537 (t0)
  outliers start: 36
  outliers final: 27
  residues processed: 212
  average time/residue: 0.2012
  time to fit residues: 62.8748
Evaluate side-chains
  212 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  270 CYS
Chi-restraints excluded: chain B residue  282 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 112 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 134 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.083860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.060104 restraints weight = 26342.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.72
r_work: 0.2702 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.5776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11412  Z= 0.148
  Angle     :  0.585  14.392  15542  Z= 0.293
  Chirality :  0.043   0.242   1780
  Planarity :  0.004   0.038   1966
  Dihedral  :  3.930  16.490   1538
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.75 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.34 (0.22), residues: 1420
  helix:  2.64 (0.23), residues: 436
  sheet:  0.80 (0.24), residues: 462
  loop : -0.55 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 167 
 HIS   0.004   0.001   HIS A  70 
 PHE   0.029   0.001   PHE A 149 
 TYR   0.014   0.001   TYR C  53 
 ARG   0.003   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03142 (  618)
  hydrogen bonds       : angle       4.14242 ( 1818)
  SS BOND              : bond        0.00342 (    8)
  SS BOND              : angle       0.90955 (   16)
  covalent geometry    : bond        0.00348 (11404)
  covalent geometry    : angle       0.58490 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 188
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.6561 (mpp-170) cc_final: 0.6266 (mtm-85)
REVERT: A  288 GLU cc_start: 0.8787 (tt0) cc_final: 0.8550 (tt0)
REVERT: A  345 ASP cc_start: 0.9266 (p0) cc_final: 0.8691 (p0)
REVERT: C   37 MET cc_start: 0.8753 (tpp) cc_final: 0.8378 (ttm)
REVERT: C   46 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8438 (mp10)
REVERT: C   83 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: C  158 GLU cc_start: 0.8646 (tp30) cc_final: 0.8170 (tp30)
REVERT: E    1 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: E  178 ASP cc_start: 0.8779 (t70) cc_final: 0.8342 (t70)
REVERT: F  176 GLN cc_start: 0.8356 (pt0) cc_final: 0.8147 (pm20)
REVERT: F  178 ASP cc_start: 0.8821 (t70) cc_final: 0.8328 (t70)
REVERT: F  212 ASP cc_start: 0.9135 (m-30) cc_final: 0.8857 (m-30)
REVERT: D   37 MET cc_start: 0.8758 (tpp) cc_final: 0.8316 (ttm)
REVERT: D   83 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8261 (mt-10)
REVERT: D  179 MET cc_start: 0.8475 (ttt) cc_final: 0.8109 (ttt)
REVERT: B   33 LYS cc_start: 0.8361 (tptp) cc_final: 0.7972 (tppt)
REVERT: B   50 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8661 (m-80)
REVERT: B   71 MET cc_start: 0.9209 (mmm) cc_final: 0.8904 (mmp)
REVERT: B  264 MET cc_start: 0.6575 (mmp) cc_final: 0.6292 (mmm)
REVERT: B  323 GLU cc_start: 0.8503 (tt0) cc_final: 0.8251 (tt0)
REVERT: B  347 ASP cc_start: 0.8815 (t0) cc_final: 0.8512 (t0)
  outliers start: 37
  outliers final: 30
  residues processed: 209
  average time/residue: 0.2015
  time to fit residues: 62.0663
Evaluate side-chains
  216 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  270 CYS
Chi-restraints excluded: chain B residue  282 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 136 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.083787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.060425 restraints weight = 26212.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.63
r_work: 0.2710 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.5890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11412  Z= 0.152
  Angle     :  0.611  15.319  15542  Z= 0.302
  Chirality :  0.043   0.203   1780
  Planarity :  0.004   0.038   1966
  Dihedral  :  3.904  16.299   1538
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.99 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.35 (0.22), residues: 1420
  helix:  2.67 (0.23), residues: 436
  sheet:  0.78 (0.24), residues: 462
  loop : -0.52 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 167 
 HIS   0.005   0.001   HIS A  70 
 PHE   0.029   0.001   PHE B 120 
 TYR   0.014   0.001   TYR C  53 
 ARG   0.003   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  618)
  hydrogen bonds       : angle       4.11484 ( 1818)
  SS BOND              : bond        0.00326 (    8)
  SS BOND              : angle       0.89692 (   16)
  covalent geometry    : bond        0.00356 (11404)
  covalent geometry    : angle       0.61026 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 193
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.6543 (mpp-170) cc_final: 0.6276 (mtm-85)
REVERT: A  288 GLU cc_start: 0.8766 (tt0) cc_final: 0.8524 (tt0)
REVERT: A  345 ASP cc_start: 0.9272 (p0) cc_final: 0.8702 (p0)
REVERT: C   37 MET cc_start: 0.8750 (tpp) cc_final: 0.8329 (ttm)
REVERT: C   46 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8475 (mp10)
REVERT: C   83 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7876 (mt-10)
REVERT: C  154 ILE cc_start: 0.8876 (mt) cc_final: 0.8640 (tt)
REVERT: C  158 GLU cc_start: 0.8657 (tp30) cc_final: 0.8154 (tp30)
REVERT: C  179 MET cc_start: 0.8942 (tpp) cc_final: 0.8041 (tpp)
REVERT: E    1 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: E  178 ASP cc_start: 0.8798 (t70) cc_final: 0.8358 (t70)
REVERT: F  178 ASP cc_start: 0.8833 (t70) cc_final: 0.8344 (t70)
REVERT: F  212 ASP cc_start: 0.9159 (m-30) cc_final: 0.8876 (m-30)
REVERT: D   37 MET cc_start: 0.8773 (tpp) cc_final: 0.8270 (ttm)
REVERT: D   83 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8224 (mt-10)
REVERT: D  149 ASN cc_start: 0.9081 (t0) cc_final: 0.8444 (t0)
REVERT: D  179 MET cc_start: 0.8452 (ttt) cc_final: 0.8074 (ttt)
REVERT: B   33 LYS cc_start: 0.8384 (tptp) cc_final: 0.7993 (tppt)
REVERT: B   50 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8652 (m-80)
REVERT: B   71 MET cc_start: 0.9211 (mmm) cc_final: 0.8661 (ttp)
REVERT: B  264 MET cc_start: 0.6557 (mmp) cc_final: 0.6311 (mmm)
REVERT: B  323 GLU cc_start: 0.8505 (tt0) cc_final: 0.8259 (tt0)
REVERT: B  347 ASP cc_start: 0.8767 (t0) cc_final: 0.8457 (t0)
  outliers start: 34
  outliers final: 30
  residues processed: 212
  average time/residue: 0.2192
  time to fit residues: 68.1047
Evaluate side-chains
  214 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  270 CYS
Chi-restraints excluded: chain B residue  282 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 11 optimal weight:   20.0000
   chunk 105 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 133 optimal weight:    0.1980
   chunk 73 optimal weight:    1.9990
   chunk 81 optimal weight:    0.2980
   chunk 57 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.084475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.061283 restraints weight = 26133.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.65
r_work: 0.2740 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.5984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11412  Z= 0.128
  Angle     :  0.613  15.965  15542  Z= 0.303
  Chirality :  0.044   0.267   1780
  Planarity :  0.004   0.039   1966
  Dihedral  :  3.813  16.102   1538
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.95 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.40 (0.22), residues: 1420
  helix:  2.67 (0.23), residues: 436
  sheet:  0.83 (0.24), residues: 462
  loop : -0.48 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 167 
 HIS   0.002   0.000   HIS A 325 
 PHE   0.032   0.002   PHE A 149 
 TYR   0.015   0.001   TYR C  53 
 ARG   0.011   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03080 (  618)
  hydrogen bonds       : angle       4.05027 ( 1818)
  SS BOND              : bond        0.00322 (    8)
  SS BOND              : angle       0.87309 (   16)
  covalent geometry    : bond        0.00300 (11404)
  covalent geometry    : angle       0.61240 (15526)

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

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

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2840 Ramachandran restraints generated.
    1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 190
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.6644 (mpp-170) cc_final: 0.6354 (mtm-85)
REVERT: A  122 ILE cc_start: 0.9339 (tt) cc_final: 0.9109 (pt)
REVERT: A  288 GLU cc_start: 0.8737 (tt0) cc_final: 0.8507 (tt0)
REVERT: A  345 ASP cc_start: 0.9248 (p0) cc_final: 0.8718 (p0)
REVERT: C   37 MET cc_start: 0.8693 (tpp) cc_final: 0.8301 (ttm)
REVERT: C   46 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8464 (mp10)
REVERT: C   83 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7926 (mt-10)
REVERT: C  154 ILE cc_start: 0.8835 (mt) cc_final: 0.8607 (tt)
REVERT: C  158 GLU cc_start: 0.8635 (tp30) cc_final: 0.8089 (tp30)
REVERT: C  179 MET cc_start: 0.8966 (tpp) cc_final: 0.8066 (tpp)
REVERT: E    1 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: E  178 ASP cc_start: 0.8802 (t70) cc_final: 0.8336 (t70)
REVERT: F  178 ASP cc_start: 0.8789 (t70) cc_final: 0.8337 (t70)
REVERT: F  212 ASP cc_start: 0.9147 (m-30) cc_final: 0.8854 (m-30)
REVERT: D   37 MET cc_start: 0.8721 (tpp) cc_final: 0.8236 (ttm)
REVERT: D  149 ASN cc_start: 0.9078 (t0) cc_final: 0.8459 (t0)
REVERT: D  179 MET cc_start: 0.8418 (ttt) cc_final: 0.8083 (ttt)
REVERT: B   33 LYS cc_start: 0.8367 (tptp) cc_final: 0.7907 (tptt)
REVERT: B   50 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8708 (m-80)
REVERT: B   71 MET cc_start: 0.9149 (mmm) cc_final: 0.8853 (mmp)
REVERT: B  264 MET cc_start: 0.6428 (mmp) cc_final: 0.6176 (mmm)
REVERT: B  323 GLU cc_start: 0.8510 (tt0) cc_final: 0.8243 (tt0)
  outliers start: 30
  outliers final: 26
  residues processed: 207
  average time/residue: 0.3651
  time to fit residues: 109.5046
Evaluate side-chains
  218 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 1.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   45 ASN
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  137 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   46 GLN
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  145 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  214 ASN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   50 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  270 CYS
Chi-restraints excluded: chain B residue  282 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0050
   chunk 105 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 HIS
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.084501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.061488 restraints weight = 25929.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.60
r_work: 0.2742 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.6064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11412  Z= 0.133
  Angle     :  0.616  15.785  15542  Z= 0.304
  Chirality :  0.044   0.243   1780
  Planarity :  0.004   0.048   1966
  Dihedral  :  3.804  17.048   1538
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.12 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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:  1.44 (0.22), residues: 1420
  helix:  2.66 (0.23), residues: 436
  sheet:  0.86 (0.24), residues: 468
  loop : -0.44 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 167 
 HIS   0.017   0.001   HIS A  70 
 PHE   0.030   0.001   PHE B 120 
 TYR   0.014   0.001   TYR C  53 
 ARG   0.011   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03127 (  618)
  hydrogen bonds       : angle       4.04361 ( 1818)
  SS BOND              : bond        0.00316 (    8)
  SS BOND              : angle       0.84111 (   16)
  covalent geometry    : bond        0.00313 (11404)
  covalent geometry    : angle       0.61595 (15526)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5697.28 seconds
wall clock time: 101 minutes 12.51 seconds (6072.51 seconds total)