Starting phenix.real_space_refine
on Wed Jul 30 07:19:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymx_39410/07_2025/8ymx_39410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymx_39410/07_2025/8ymx_39410.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymx_39410/07_2025/8ymx_39410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymx_39410/07_2025/8ymx_39410.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymx_39410/07_2025/8ymx_39410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymx_39410/07_2025/8ymx_39410.cif"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5232      2.51       5
     N    1374      2.21       5
     O    1521      1.98       5
     H    3957      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12138
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 4046
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 17, 'TRANS': 320}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 7.60, per 1000 atoms: 0.63
  Number of scatterers: 12138
  At special positions: 0
  Unit cell: (101.37, 106.95, 96.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     O    1521      8.00
     N    1374      7.00
     C    5232      6.00
     H    3957      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 106 " - pdb=" SG  CYS C 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 106 " - pdb=" SG  CYS B 188 " 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: 3.02
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 12 sheets defined
      35.3% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 82
      removed outlier: 3.612A  pdb=" N   LEU A  82 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 124
    Processing helix  chain 'A' and resid 129 through 133
      removed outlier: 3.747A  pdb=" N   ASP A 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 133 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 129 through 133'
    Processing helix  chain 'A' and resid 140 through 146
    Processing helix  chain 'A' and resid 147 through 149
      No H-bonds generated for 'chain 'A' and resid 147 through 149'
    Processing helix  chain 'A' and resid 212 through 217
      removed outlier: 3.850A  pdb=" N   ASP A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.502A  pdb=" N   SER A 237 " --> pdb=" O   HIS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 295
      removed outlier: 3.813A  pdb=" N   ALA A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 3.703A  pdb=" N   LYS A 307 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 308 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 308'
    Processing helix  chain 'A' and resid 315 through 328
      removed outlier: 3.761A  pdb=" N   PHE A 321 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 400
      removed outlier: 4.206A  pdb=" N   ARG A 384 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLY A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLY A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 82
      removed outlier: 3.612A  pdb=" N   LEU B  82 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 124
    Processing helix  chain 'B' and resid 129 through 133
      removed outlier: 3.747A  pdb=" N   ASP B 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU B 133 " --> pdb=" O   PHE B 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 133'
    Processing helix  chain 'B' and resid 140 through 146
    Processing helix  chain 'B' and resid 147 through 149
      No H-bonds generated for 'chain 'B' and resid 147 through 149'
    Processing helix  chain 'B' and resid 212 through 217
      removed outlier: 3.850A  pdb=" N   ASP B 217 " --> pdb=" O   ARG B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 240
      removed outlier: 3.502A  pdb=" N   SER B 237 " --> pdb=" O   HIS B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 295
      removed outlier: 3.814A  pdb=" N   ALA B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.703A  pdb=" N   LYS B 307 " --> pdb=" O   MET B 304 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 308 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 304 through 308'
    Processing helix  chain 'B' and resid 315 through 328
      removed outlier: 3.760A  pdb=" N   PHE B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 400
      removed outlier: 4.206A  pdb=" N   ARG B 384 " --> pdb=" O   THR B 380 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY B 385 " --> pdb=" O   TYR B 381 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLY B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   GLY B 392 " --> pdb=" O   SER B 388 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL B 393 " --> pdb=" O   ASP B 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 82
      removed outlier: 3.612A  pdb=" N   LEU C  82 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 124
    Processing helix  chain 'C' and resid 129 through 133
      removed outlier: 3.747A  pdb=" N   ASP C 132 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU C 133 " --> pdb=" O   PHE C 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 129 through 133'
    Processing helix  chain 'C' and resid 140 through 146
    Processing helix  chain 'C' and resid 147 through 149
      No H-bonds generated for 'chain 'C' and resid 147 through 149'
    Processing helix  chain 'C' and resid 212 through 217
      removed outlier: 3.851A  pdb=" N   ASP C 217 " --> pdb=" O   ARG C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 240
      removed outlier: 3.503A  pdb=" N   SER C 237 " --> pdb=" O   HIS C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 295
      removed outlier: 3.813A  pdb=" N   ALA C 281 " --> pdb=" O   GLU C 277 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 308
      removed outlier: 3.702A  pdb=" N   LYS C 307 " --> pdb=" O   MET C 304 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU C 308 " --> pdb=" O   ARG C 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 304 through 308'
    Processing helix  chain 'C' and resid 315 through 328
      removed outlier: 3.760A  pdb=" N   PHE C 321 " --> pdb=" O   ALA C 317 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 400
      removed outlier: 4.205A  pdb=" N   ARG C 384 " --> pdb=" O   THR C 380 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY C 385 " --> pdb=" O   TYR C 381 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   GLY C 391 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   GLY C 392 " --> pdb=" O   SER C 388 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL C 393 " --> pdb=" O   ASP C 389 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94
      removed outlier: 3.776A  pdb=" N   ARG A  89 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98
    Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181
      removed outlier: 3.580A  pdb=" N   HIS A 179 " --> pdb=" O   ASN A 190 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A 189 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 105 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE A 103 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 160
    Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 94
      removed outlier: 3.777A  pdb=" N   ARG B  89 " --> pdb=" O   THR B 376 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 181
      removed outlier: 3.580A  pdb=" N   HIS B 179 " --> pdb=" O   ASN B 190 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE B 189 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL B 105 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE B 103 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 160
    Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 94
      removed outlier: 3.776A  pdb=" N   ARG C  89 " --> pdb=" O   THR C 376 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 98
    Processing sheet with id=AB2, first strand: chain 'C' and resid 179 through 181
      removed outlier: 3.579A  pdb=" N   HIS C 179 " --> pdb=" O   ASN C 190 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE C 189 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL C 105 " --> pdb=" O   ILE C 189 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE C 103 " --> pdb=" O   ILE C 191 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 155 through 160

    307 hydrogen bonds defined for protein.
    849 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: 3.98

  Time building geometry restraints manager: 3.67 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3948
        1.03 -     1.23: 17
        1.23 -     1.42: 3583
        1.42 -     1.62: 4707
        1.62 -     1.82: 78
  Bond restraints: 12333
  Sorted by residual:
  bond pdb=" N   PHE C 354 "
       pdb=" CA  PHE C 354 "
    ideal  model  delta    sigma   weight residual
    1.462  1.483 -0.022 1.46e-02 4.69e+03 2.20e+00
  bond pdb=" N   PHE A 354 "
       pdb=" CA  PHE A 354 "
    ideal  model  delta    sigma   weight residual
    1.462  1.483 -0.021 1.46e-02 4.69e+03 2.13e+00
  bond pdb=" N   PHE B 354 "
       pdb=" CA  PHE B 354 "
    ideal  model  delta    sigma   weight residual
    1.462  1.483 -0.021 1.46e-02 4.69e+03 2.12e+00
  bond pdb=" C   GLN B 212 "
       pdb=" N   PRO B 213 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.013 1.27e-02 6.20e+03 1.11e+00
  bond pdb=" C   GLN C 212 "
       pdb=" N   PRO C 213 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.013 1.27e-02 6.20e+03 1.07e+00
  ... (remaining 12328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.14: 20286
        7.14 -    14.27: 0
       14.27 -    21.41: 3
       21.41 -    28.55: 9
       28.55 -    35.69: 27
  Bond angle restraints: 20325
  Sorted by residual:
  angle pdb=" N   ILE A 320 "
        pdb=" CA  ILE A 320 "
        pdb=" HA  ILE A 320 "
      ideal   model   delta    sigma   weight residual
     110.00   74.31   35.69 3.00e+00 1.11e-01 1.41e+02
  angle pdb=" N   ILE C 320 "
        pdb=" CA  ILE C 320 "
        pdb=" HA  ILE C 320 "
      ideal   model   delta    sigma   weight residual
     110.00   74.32   35.68 3.00e+00 1.11e-01 1.41e+02
  angle pdb=" N   ILE B 320 "
        pdb=" CA  ILE B 320 "
        pdb=" HA  ILE B 320 "
      ideal   model   delta    sigma   weight residual
     110.00   74.32   35.68 3.00e+00 1.11e-01 1.41e+02
  angle pdb=" C   GLN B 212 "
        pdb=" CA  GLN B 212 "
        pdb=" HA  GLN B 212 "
      ideal   model   delta    sigma   weight residual
     109.00   73.51   35.49 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" C   GLN C 212 "
        pdb=" CA  GLN C 212 "
        pdb=" HA  GLN C 212 "
      ideal   model   delta    sigma   weight residual
     109.00   73.53   35.47 3.00e+00 1.11e-01 1.40e+02
  ... (remaining 20320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5570
       17.81 -    35.63: 653
       35.63 -    53.44: 170
       53.44 -    71.25: 33
       71.25 -    89.06: 24
  Dihedral angle restraints: 6450
    sinusoidal: 3102
      harmonic: 3348
  Sorted by residual:
  dihedral pdb=" CA  ARG C  89 "
           pdb=" C   ARG C  89 "
           pdb=" N   ILE C  90 "
           pdb=" CA  ILE C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.19   21.81     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  ARG B  89 "
           pdb=" C   ARG B  89 "
           pdb=" N   ILE B  90 "
           pdb=" CA  ILE B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.20   21.80     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  ARG A  89 "
           pdb=" C   ARG A  89 "
           pdb=" N   ILE A  90 "
           pdb=" CA  ILE A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.20   21.80     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 6447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.328: 1263
       0.328 -    0.656: 6
       0.656 -    0.985: 0
       0.985 -    1.313: 0
       1.313 -    1.641: 3
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CB  ILE C 320 "
            pdb=" CA  ILE C 320 "
            pdb=" CG1 ILE C 320 "
            pdb=" CG2 ILE C 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.00    1.64 2.00e-01 2.50e+01 6.73e+01
  chirality pdb=" CB  ILE A 320 "
            pdb=" CA  ILE A 320 "
            pdb=" CG1 ILE A 320 "
            pdb=" CG2 ILE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.00    1.64 2.00e-01 2.50e+01 6.72e+01
  chirality pdb=" CB  ILE B 320 "
            pdb=" CA  ILE B 320 "
            pdb=" CG1 ILE B 320 "
            pdb=" CG2 ILE B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.01    1.64 2.00e-01 2.50e+01 6.72e+01
  ... (remaining 1269 not shown)

  Planarity restraints: 1953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 212 "   -0.022 2.00e-02 2.50e+03   4.41e-02 1.94e+01
        pdb=" C   GLN B 212 "    0.076 2.00e-02 2.50e+03
        pdb=" O   GLN B 212 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   PRO B 213 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 212 "   -0.022 2.00e-02 2.50e+03   4.40e-02 1.94e+01
        pdb=" C   GLN C 212 "    0.076 2.00e-02 2.50e+03
        pdb=" O   GLN C 212 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   PRO C 213 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 212 "    0.022 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        pdb=" C   GLN A 212 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   GLN A 212 "    0.029 2.00e-02 2.50e+03
        pdb=" N   PRO A 213 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1950 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.13: 314
        2.13 -     2.75: 15633
        2.75 -     3.37: 29468
        3.37 -     3.98: 38908
        3.98 -     4.60: 59390
  Nonbonded interactions: 143713
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 161 "
            pdb=" H   ILE B 198 "
     model   vdw
     1.516 2.450
  nonbonded pdb=" OE1 GLU C 161 "
            pdb=" H   ILE C 198 "
     model   vdw
     1.516 2.450
  nonbonded pdb=" OE1 GLU A 161 "
            pdb=" H   ILE A 198 "
     model   vdw
     1.516 2.450
  nonbonded pdb="HH12 ARG A  89 "
            pdb=" OE2 GLU B 377 "
     model   vdw
     1.531 2.450
  nonbonded pdb=" HA  ILE C 320 "
            pdb=" HB  ILE C 320 "
     model   vdw
     1.537 1.952
  ... (remaining 143708 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             1.080
  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:             0.230
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     29.240
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5677
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8379  Z= 0.154
  Angle     :  0.667  14.950  11382  Z= 0.371
  Chirality :  0.094   1.641   1272
  Planarity :  0.005   0.045   1473
  Dihedral  : 17.976  89.065   3093
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 49.90
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.48 %
    Favored  : 84.23 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 28.43 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.25), residues: 1008
  helix: -0.27 (0.30), residues: 282
  sheet: -2.66 (0.36), residues: 192
  loop : -3.32 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 145 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.031   0.001   PHE A 397 
 TYR   0.012   0.001   TYR C 265 
 ARG   0.001   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12609 (  307)
  hydrogen bonds       : angle       7.09277 (  849)
  SS BOND              : bond        0.00101 (    3)
  SS BOND              : angle       1.14522 (    6)
  covalent geometry    : bond        0.00318 ( 8376)
  covalent geometry    : angle       0.66687 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  146 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 PHE cc_start: 0.6399 (m-80) cc_final: 0.6070 (m-80)
REVERT: B  397 PHE cc_start: 0.6252 (m-80) cc_final: 0.5940 (m-80)
REVERT: C  205 PHE cc_start: 0.7189 (p90) cc_final: 0.6938 (p90)
  outliers start: 3
  outliers final: 1
  residues processed: 143
  average time/residue: 0.2570
  time to fit residues: 54.1131
Evaluate side-chains
  138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0170
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0970
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4663 r_free = 0.4663 target = 0.210809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.188242 restraints weight = 24113.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.4423 rms_B_bonded: 3.39
r_work: 0.4326 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5618
moved from start:          0.0606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8379  Z= 0.137
  Angle     :  0.608  15.167  11382  Z= 0.322
  Chirality :  0.095   1.672   1272
  Planarity :  0.005   0.049   1473
  Dihedral  :  5.062  35.244   1127
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 46.26
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.38 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.07 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.26), residues: 1008
  helix:  0.03 (0.31), residues: 267
  sheet: -2.71 (0.36), residues: 189
  loop : -3.21 (0.25), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.004   TRP A 145 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.026   0.001   PHE A 397 
 TYR   0.009   0.001   TYR B 279 
 ARG   0.005   0.000   ARG A 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  307)
  hydrogen bonds       : angle       6.33497 (  849)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       0.67530 (    6)
  covalent geometry    : bond        0.00307 ( 8376)
  covalent geometry    : angle       0.60780 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  176 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 ARG cc_start: 0.2695 (OUTLIER) cc_final: 0.2427 (mtm110)
REVERT: B  229 HIS cc_start: 0.7333 (p-80) cc_final: 0.6758 (p-80)
REVERT: B  390 ILE cc_start: 0.7489 (mm) cc_final: 0.7202 (mm)
REVERT: B  397 PHE cc_start: 0.6456 (m-80) cc_final: 0.6046 (m-80)
REVERT: C  397 PHE cc_start: 0.6466 (m-80) cc_final: 0.6014 (m-80)
  outliers start: 33
  outliers final: 22
  residues processed: 166
  average time/residue: 0.2393
  time to fit residues: 59.2767
Evaluate side-chains
  164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  373 GLN
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  187 GLN
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  373 GLN
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4617 r_free = 0.4617 target = 0.205882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.182806 restraints weight = 24426.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.4381 rms_B_bonded: 3.47
r_work: 0.4281 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5688
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8379  Z= 0.193
  Angle     :  0.628  15.136  11382  Z= 0.336
  Chirality :  0.095   1.666   1272
  Planarity :  0.004   0.039   1473
  Dihedral  :  5.241  37.848   1127
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 52.49
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.67 %
    Favored  : 84.03 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 24.18 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.25), residues: 1008
  helix: -0.67 (0.29), residues: 282
  sheet: -3.07 (0.37), residues: 192
  loop : -3.16 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP C 145 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.021   0.001   PHE C 397 
 TYR   0.009   0.001   TYR B 279 
 ARG   0.002   0.000   ARG C 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  307)
  hydrogen bonds       : angle       6.19115 (  849)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.78084 (    6)
  covalent geometry    : bond        0.00425 ( 8376)
  covalent geometry    : angle       0.62750 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 145
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.4635 (OUTLIER) cc_final: 0.3932 (ptt-90)
REVERT: A  145 TRP cc_start: 0.4698 (t-100) cc_final: 0.4415 (t-100)
REVERT: A  318 ARG cc_start: 0.2733 (OUTLIER) cc_final: 0.2411 (mtm110)
REVERT: B  229 HIS cc_start: 0.7540 (p-80) cc_final: 0.6761 (p-80)
REVERT: B  397 PHE cc_start: 0.6568 (m-80) cc_final: 0.6170 (m-80)
REVERT: C  397 PHE cc_start: 0.6636 (m-80) cc_final: 0.6132 (m-80)
  outliers start: 43
  outliers final: 32
  residues processed: 178
  average time/residue: 0.2625
  time to fit residues: 67.6493
Evaluate side-chains
  178 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  187 GLN
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4597 r_free = 0.4597 target = 0.203728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.181459 restraints weight = 23922.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.4360 rms_B_bonded: 3.35
r_work: 0.4258 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5755
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8379  Z= 0.249
  Angle     :  0.677  15.384  11382  Z= 0.366
  Chirality :  0.096   1.671   1272
  Planarity :  0.005   0.047   1473
  Dihedral  :  5.672  40.209   1127
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 56.56
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 16.07 %
    Favored  : 83.63 %
  Rotamer:
    Outliers :  6.75 %
    Allowed  : 23.42 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.79 (0.25), residues: 1008
  helix: -1.11 (0.28), residues: 282
  sheet: -2.60 (0.40), residues: 177
  loop : -3.38 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.006   TRP A 145 
 HIS   0.006   0.001   HIS A 229 
 PHE   0.019   0.002   PHE A 205 
 TYR   0.013   0.002   TYR C 139 
 ARG   0.003   0.000   ARG C 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  307)
  hydrogen bonds       : angle       6.24982 (  849)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.89643 (    6)
  covalent geometry    : bond        0.00544 ( 8376)
  covalent geometry    : angle       0.67666 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 153
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LEU cc_start: 0.4430 (OUTLIER) cc_final: 0.4148 (mt)
REVERT: A  316 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6531 (t0)
REVERT: A  318 ARG cc_start: 0.2938 (OUTLIER) cc_final: 0.2539 (mtm110)
REVERT: B  108 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.2414 (ptt-90)
REVERT: B  199 TYR cc_start: 0.5177 (t80) cc_final: 0.4918 (t80)
REVERT: B  397 PHE cc_start: 0.6620 (m-80) cc_final: 0.6206 (m-80)
REVERT: C  108 ARG cc_start: 0.5465 (OUTLIER) cc_final: 0.3155 (ptt-90)
REVERT: C  120 VAL cc_start: 0.2961 (t) cc_final: 0.1454 (p)
REVERT: C  145 TRP cc_start: 0.4982 (t-100) cc_final: 0.4753 (t-100)
REVERT: C  397 PHE cc_start: 0.6605 (m-80) cc_final: 0.6300 (m-80)
  outliers start: 62
  outliers final: 44
  residues processed: 200
  average time/residue: 0.3149
  time to fit residues: 88.7141
Evaluate side-chains
  197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 148
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  207 ARG
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  373 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  373 GLN
Chi-restraints excluded: chain C residue  390 ILE
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0070
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.1980
   overall best weight:    0.3598

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4635 r_free = 0.4635 target = 0.207519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.185137 restraints weight = 24058.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.4399 rms_B_bonded: 3.41
r_work: 0.4298 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5675
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8379  Z= 0.130
  Angle     :  0.604  15.110  11382  Z= 0.319
  Chirality :  0.095   1.658   1272
  Planarity :  0.004   0.036   1473
  Dihedral  :  5.258  40.837   1127
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 49.47
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.67 %
    Favored  : 84.03 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 23.42 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.25), residues: 1008
  helix: -0.31 (0.30), residues: 267
  sheet: -2.61 (0.38), residues: 174
  loop : -3.34 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 145 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.014   0.001   PHE A 205 
 TYR   0.009   0.001   TYR B 279 
 ARG   0.002   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  307)
  hydrogen bonds       : angle       6.10822 (  849)
  SS BOND              : bond        0.00280 (    3)
  SS BOND              : angle       0.91710 (    6)
  covalent geometry    : bond        0.00297 ( 8376)
  covalent geometry    : angle       0.60373 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 143
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.4475 (OUTLIER) cc_final: 0.3875 (ptt-90)
REVERT: A  120 VAL cc_start: 0.3315 (t) cc_final: 0.2175 (p)
REVERT: A  145 TRP cc_start: 0.4716 (t-100) cc_final: 0.4511 (t-100)
REVERT: A  206 VAL cc_start: 0.7541 (p) cc_final: 0.7310 (t)
REVERT: A  318 ARG cc_start: 0.2811 (OUTLIER) cc_final: 0.2446 (mtm110)
REVERT: B  108 ARG cc_start: 0.5156 (OUTLIER) cc_final: 0.4586 (mtt90)
REVERT: B  397 PHE cc_start: 0.6613 (m-80) cc_final: 0.6159 (m-80)
REVERT: C  108 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.1525 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3184 (t) cc_final: 0.1778 (p)
REVERT: C  340 LYS cc_start: 0.4548 (OUTLIER) cc_final: 0.3996 (ptpp)
REVERT: C  397 PHE cc_start: 0.6642 (m-80) cc_final: 0.6210 (m-80)
  outliers start: 58
  outliers final: 43
  residues processed: 188
  average time/residue: 0.3378
  time to fit residues: 92.7822
Evaluate side-chains
  191 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 143
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  373 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  187 GLN
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  373 GLN
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 98 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 2 optimal weight:    0.2980
   chunk 32 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4624 r_free = 0.4624 target = 0.206407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.183643 restraints weight = 24497.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.4392 rms_B_bonded: 3.45
r_work: 0.4291 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5686
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8379  Z= 0.144
  Angle     :  0.604  15.329  11382  Z= 0.319
  Chirality :  0.095   1.679   1272
  Planarity :  0.004   0.037   1473
  Dihedral  :  5.246  41.200   1127
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 49.96
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.67 %
    Favored  : 84.03 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 23.97 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.26), residues: 1008
  helix: -0.27 (0.31), residues: 267
  sheet: -2.50 (0.39), residues: 180
  loop : -3.34 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.005   TRP B 145 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.015   0.001   PHE A 205 
 TYR   0.010   0.001   TYR B 199 
 ARG   0.001   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  307)
  hydrogen bonds       : angle       6.01411 (  849)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       1.17173 (    6)
  covalent geometry    : bond        0.00325 ( 8376)
  covalent geometry    : angle       0.60342 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 150
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.4512 (OUTLIER) cc_final: 0.3959 (ptt-90)
REVERT: A  120 VAL cc_start: 0.3328 (t) cc_final: 0.2098 (p)
REVERT: A  145 TRP cc_start: 0.4812 (t-100) cc_final: 0.4546 (t-100)
REVERT: A  197 LEU cc_start: 0.4352 (OUTLIER) cc_final: 0.4083 (mt)
REVERT: A  318 ARG cc_start: 0.2759 (OUTLIER) cc_final: 0.2378 (mtm110)
REVERT: B  108 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.4529 (mtt90)
REVERT: B  397 PHE cc_start: 0.6684 (m-80) cc_final: 0.6191 (m-80)
REVERT: C  108 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.1543 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3160 (t) cc_final: 0.1748 (p)
REVERT: C  340 LYS cc_start: 0.4593 (OUTLIER) cc_final: 0.4055 (ptpp)
REVERT: C  397 PHE cc_start: 0.6606 (m-80) cc_final: 0.6176 (m-80)
  outliers start: 57
  outliers final: 46
  residues processed: 193
  average time/residue: 0.2789
  time to fit residues: 76.3198
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 148
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  373 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  373 GLN
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0020
   chunk 57 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    0.2980
   chunk 84 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0270
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.3046

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4657 r_free = 0.4657 target = 0.210156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.187807 restraints weight = 24060.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4419 rms_B_bonded: 3.41
r_work: 0.4319 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5637
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8379  Z= 0.113
  Angle     :  0.586  15.049  11382  Z= 0.307
  Chirality :  0.094   1.656   1272
  Planarity :  0.004   0.042   1473
  Dihedral  :  5.042  41.363   1127
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 47.50
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 14.38 %
    Favored  : 85.32 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 24.40 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.26), residues: 1008
  helix:  0.04 (0.31), residues: 267
  sheet: -2.46 (0.39), residues: 180
  loop : -3.27 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP C 145 
 HIS   0.003   0.001   HIS C 229 
 PHE   0.012   0.001   PHE A 205 
 TYR   0.008   0.001   TYR B 279 
 ARG   0.003   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03213 (  307)
  hydrogen bonds       : angle       5.89458 (  849)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       0.99370 (    6)
  covalent geometry    : bond        0.00262 ( 8376)
  covalent geometry    : angle       0.58525 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 147
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 VAL cc_start: 0.3320 (t) cc_final: 0.2091 (p)
REVERT: A  145 TRP cc_start: 0.4661 (t-100) cc_final: 0.4416 (t-100)
REVERT: A  206 VAL cc_start: 0.7553 (p) cc_final: 0.7304 (t)
REVERT: A  318 ARG cc_start: 0.2673 (OUTLIER) cc_final: 0.2304 (mtm110)
REVERT: B  108 ARG cc_start: 0.4722 (OUTLIER) cc_final: 0.4378 (mtt90)
REVERT: B  397 PHE cc_start: 0.6632 (m-80) cc_final: 0.6153 (m-80)
REVERT: C  108 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.1368 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3176 (t) cc_final: 0.1747 (p)
REVERT: C  145 TRP cc_start: 0.4850 (t-100) cc_final: 0.3230 (t60)
REVERT: C  241 THR cc_start: 0.4365 (m) cc_final: 0.3948 (m)
REVERT: C  340 LYS cc_start: 0.4545 (OUTLIER) cc_final: 0.3986 (ptpp)
REVERT: C  397 PHE cc_start: 0.6611 (m-80) cc_final: 0.6161 (m-80)
  outliers start: 53
  outliers final: 40
  residues processed: 187
  average time/residue: 0.2735
  time to fit residues: 74.5443
Evaluate side-chains
  185 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 141
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  373 GLN
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  373 GLN
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0670
   chunk 65 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4601 r_free = 0.4601 target = 0.203833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.181243 restraints weight = 24170.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4368 rms_B_bonded: 3.45
r_work: 0.4267 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8379  Z= 0.232
  Angle     :  0.656  15.122  11382  Z= 0.352
  Chirality :  0.095   1.661   1272
  Planarity :  0.004   0.035   1473
  Dihedral  :  5.516  42.170   1127
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 56.13
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 16.67 %
    Favored  : 83.04 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 23.75 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.25), residues: 1008
  helix: -0.76 (0.29), residues: 282
  sheet: -2.98 (0.36), residues: 198
  loop : -3.32 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.007   TRP C 145 
 HIS   0.006   0.001   HIS A 229 
 PHE   0.019   0.002   PHE A 205 
 TYR   0.010   0.001   TYR C 139 
 ARG   0.003   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  307)
  hydrogen bonds       : angle       6.04478 (  849)
  SS BOND              : bond        0.00329 (    3)
  SS BOND              : angle       1.02424 (    6)
  covalent geometry    : bond        0.00509 ( 8376)
  covalent geometry    : angle       0.65560 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 152
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.4621 (OUTLIER) cc_final: 0.4295 (ptt-90)
REVERT: A  120 VAL cc_start: 0.3452 (t) cc_final: 0.2033 (p)
REVERT: A  145 TRP cc_start: 0.4837 (t-100) cc_final: 0.4583 (t-100)
REVERT: A  197 LEU cc_start: 0.4478 (OUTLIER) cc_final: 0.4215 (mt)
REVERT: A  318 ARG cc_start: 0.2910 (OUTLIER) cc_final: 0.2461 (mtm110)
REVERT: B  108 ARG cc_start: 0.5336 (OUTLIER) cc_final: 0.2339 (ptt-90)
REVERT: B  397 PHE cc_start: 0.6731 (m-80) cc_final: 0.6244 (m-80)
REVERT: C  108 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.1691 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3337 (t) cc_final: 0.1822 (p)
REVERT: C  340 LYS cc_start: 0.4724 (OUTLIER) cc_final: 0.4232 (pttm)
REVERT: C  397 PHE cc_start: 0.6736 (m-80) cc_final: 0.6273 (m-80)
  outliers start: 60
  outliers final: 48
  residues processed: 198
  average time/residue: 0.3239
  time to fit residues: 88.3936
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 152
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  139 TYR
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  378 TYR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   chunk 67 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4632 r_free = 0.4632 target = 0.207624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.185257 restraints weight = 24207.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4394 rms_B_bonded: 3.43
r_work: 0.4294 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5689
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8379  Z= 0.147
  Angle     :  0.610  15.041  11382  Z= 0.321
  Chirality :  0.094   1.656   1272
  Planarity :  0.004   0.065   1473
  Dihedral  :  5.329  43.033   1127
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 51.57
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 14.58 %
    Favored  : 85.12 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 25.16 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.42 (0.26), residues: 1008
  helix: -0.27 (0.31), residues: 267
  sheet: -2.53 (0.38), residues: 180
  loop : -3.35 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP C 145 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.013   0.001   PHE A 205 
 TYR   0.010   0.001   TYR C 139 
 ARG   0.002   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  307)
  hydrogen bonds       : angle       5.96216 (  849)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       1.01071 (    6)
  covalent geometry    : bond        0.00331 ( 8376)
  covalent geometry    : angle       0.60956 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 146
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.4541 (OUTLIER) cc_final: 0.4042 (ptt-90)
REVERT: A  120 VAL cc_start: 0.3382 (t) cc_final: 0.2065 (p)
REVERT: A  145 TRP cc_start: 0.4748 (t-100) cc_final: 0.4467 (t-100)
REVERT: A  206 VAL cc_start: 0.7505 (p) cc_final: 0.7265 (t)
REVERT: A  318 ARG cc_start: 0.2826 (OUTLIER) cc_final: 0.2380 (mtm110)
REVERT: B  108 ARG cc_start: 0.5189 (OUTLIER) cc_final: 0.4758 (mtt90)
REVERT: B  397 PHE cc_start: 0.6706 (m-80) cc_final: 0.6228 (m-80)
REVERT: C  108 ARG cc_start: 0.5143 (OUTLIER) cc_final: 0.1497 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3315 (t) cc_final: 0.1819 (p)
REVERT: C  340 LYS cc_start: 0.4688 (OUTLIER) cc_final: 0.4297 (ptpp)
REVERT: C  397 PHE cc_start: 0.6674 (m-80) cc_final: 0.6189 (m-80)
  outliers start: 51
  outliers final: 42
  residues processed: 187
  average time/residue: 0.2987
  time to fit residues: 79.5778
Evaluate side-chains
  193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 146
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  139 TYR
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  268 LYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4616 r_free = 0.4616 target = 0.206005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.183815 restraints weight = 24140.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.4378 rms_B_bonded: 3.41
r_work: 0.4275 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5722
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8379  Z= 0.196
  Angle     :  0.635  15.040  11382  Z= 0.337
  Chirality :  0.095   1.657   1272
  Planarity :  0.004   0.051   1473
  Dihedral  :  5.479  43.441   1127
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 54.10
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.77 %
    Favored  : 83.93 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 24.51 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.25), residues: 1008
  helix: -0.73 (0.29), residues: 282
  sheet: -2.68 (0.38), residues: 177
  loop : -3.34 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.006   TRP C 145 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.015   0.001   PHE A 205 
 TYR   0.010   0.001   TYR C 139 
 ARG   0.002   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  307)
  hydrogen bonds       : angle       6.02216 (  849)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       1.01238 (    6)
  covalent geometry    : bond        0.00434 ( 8376)
  covalent geometry    : angle       0.63483 (11376)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Residue THR  344 is missing expected H atoms. Skipping.
Evaluate side-chains
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 150
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.4559 (OUTLIER) cc_final: 0.4139 (ptt-90)
REVERT: A  120 VAL cc_start: 0.3423 (t) cc_final: 0.2016 (p)
REVERT: A  145 TRP cc_start: 0.4816 (t-100) cc_final: 0.4553 (t-100)
REVERT: A  206 VAL cc_start: 0.7479 (p) cc_final: 0.7253 (t)
REVERT: A  318 ARG cc_start: 0.2909 (OUTLIER) cc_final: 0.2407 (mtm110)
REVERT: B  108 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.4652 (mtt90)
REVERT: B  397 PHE cc_start: 0.6764 (m-80) cc_final: 0.6256 (m-80)
REVERT: C  108 ARG cc_start: 0.5229 (OUTLIER) cc_final: 0.1583 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3362 (t) cc_final: 0.1836 (p)
REVERT: C  340 LYS cc_start: 0.4757 (OUTLIER) cc_final: 0.4438 (ptpp)
REVERT: C  397 PHE cc_start: 0.6725 (m-80) cc_final: 0.6277 (m-80)
  outliers start: 55
  outliers final: 48
  residues processed: 192
  average time/residue: 0.3032
  time to fit residues: 81.0209
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 149
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  270 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   65 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  139 TYR
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  269 THR
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  316 ASP
Chi-restraints excluded: chain B residue  340 LYS
Chi-restraints excluded: chain B residue  373 GLN
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  106 CYS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  248 VAL
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  268 LYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  364 SER
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  378 TYR
Chi-restraints excluded: chain C residue  394 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 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 = 0.4617 r_free = 0.4617 target = 0.205799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.183409 restraints weight = 24157.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4386 rms_B_bonded: 3.41
r_work: 0.4284 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5702
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8379  Z= 0.161
  Angle     :  0.618  15.050  11382  Z= 0.326
  Chirality :  0.094   1.658   1272
  Planarity :  0.004   0.059   1473
  Dihedral  :  5.423  44.065   1127
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 53.05
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.97 %
    Favored  : 83.73 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 24.29 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.26), residues: 1008
  helix: -0.37 (0.31), residues: 267
  sheet: -2.57 (0.38), residues: 180
  loop : -3.35 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.005   TRP C 145 
 HIS   0.005   0.001   HIS A 229 
 PHE   0.013   0.001   PHE A 205 
 TYR   0.010   0.001   TYR C 139 
 ARG   0.002   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03407 (  307)
  hydrogen bonds       : angle       5.98776 (  849)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.98482 (    6)
  covalent geometry    : bond        0.00362 ( 8376)
  covalent geometry    : angle       0.61821 (11376)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5833.59 seconds
wall clock time: 103 minutes 47.51 seconds (6227.51 seconds total)