Starting phenix.real_space_refine
on Wed May 14 18:42:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymx_39410/05_2025/8ymx_39410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymx_39410/05_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_39410/05_2025/8ymx_39410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymx_39410/05_2025/8ymx_39410.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymx_39410/05_2025/8ymx_39410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymx_39410/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.80, per 1000 atoms: 0.64
  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: 3.05
  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: 1.01
  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: 3.56

  Time building geometry restraints manager: 3.62 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: 0.06
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:             0.660
  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:             0.240
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.330
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.660
-------------------------------------------------------------------------------
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  : 0.991 
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: 0.2500
  time to fit residues: 52.4550
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  : 1.003 
-------------------------------------------------------------------------------
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 = 0.4662 r_free = 0.4662 target = 0.210717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.188141 restraints weight = 24106.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.4423 rms_B_bonded: 3.39
r_work: 0.4325 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5619
moved from start:          0.0599

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= 0.135
  Angle     :  0.608  15.170  11382  Z= 0.322
  Chirality :  0.095   1.672   1272
  Planarity :  0.005   0.049   1473
  Dihedral  :  5.061  35.183   1127
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 46.45
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.38 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.40 %
    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 : -3.22 (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   0.008   0.001   TYR B 279 
 ARG   0.005   0.000   ARG A 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  307)
  hydrogen bonds       : angle       6.34174 (  849)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       0.66948 (    6)
  covalent geometry    : bond        0.00306 ( 8376)
  covalent geometry    : angle       0.60770 (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
  174 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.981 
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  318 ARG cc_start: 0.2697 (OUTLIER) cc_final: 0.2428 (mtm110)
REVERT: B  229 HIS cc_start: 0.7339 (p-80) cc_final: 0.6768 (p-80)
REVERT: B  390 ILE cc_start: 0.7482 (mm) cc_final: 0.7192 (mm)
REVERT: B  397 PHE cc_start: 0.6460 (m-80) cc_final: 0.6049 (m-80)
REVERT: C  397 PHE cc_start: 0.6458 (m-80) cc_final: 0.6007 (m-80)
  outliers start: 30
  outliers final: 21
  residues processed: 164
  average time/residue: 0.2343
  time to fit residues: 57.0236
Evaluate side-chains
  164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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  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:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0670
   chunk 79 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0070
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 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 = 0.4646 r_free = 0.4646 target = 0.209264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.186400 restraints weight = 24382.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.4409 rms_B_bonded: 3.44
r_work: 0.4309 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5639
moved from start:          0.0871

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= 0.142
  Angle     :  0.598  15.066  11382  Z= 0.317
  Chirality :  0.095   1.662   1272
  Planarity :  0.004   0.039   1473
  Dihedral  :  5.033  37.401   1127
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 47.37
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.38 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.29 %
    Favored  : 71.68 %
  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: -3.20 (0.26), residues: 1008
  helix: -0.09 (0.31), residues: 267
  sheet: -2.16 (0.41), residues: 174
  loop : -3.30 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP C 145 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.021   0.001   PHE C 397 
 TYR   0.008   0.001   TYR B 279 
 ARG   0.002   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  307)
  hydrogen bonds       : angle       6.14299 (  849)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       0.65768 (    6)
  covalent geometry    : bond        0.00319 ( 8376)
  covalent geometry    : angle       0.59796 (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
  182 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 1.026 
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: symmetry clash
   revert: symmetry clash
REVERT: A  145 TRP cc_start: 0.4637 (t-100) cc_final: 0.4307 (t-100)
REVERT: A  318 ARG cc_start: 0.2593 (OUTLIER) cc_final: 0.2308 (mtm110)
REVERT: B  229 HIS cc_start: 0.7406 (p-80) cc_final: 0.6705 (p-80)
REVERT: B  397 PHE cc_start: 0.6510 (m-80) cc_final: 0.6090 (m-80)
REVERT: C  397 PHE cc_start: 0.6575 (m-80) cc_final: 0.6066 (m-80)
  outliers start: 37
  outliers final: 31
  residues processed: 171
  average time/residue: 0.2972
  time to fit residues: 74.2331
Evaluate side-chains
  176 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
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  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  313 THR
Chi-restraints excluded: chain A residue  316 ASP
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  120 VAL
Chi-restraints excluded: chain C residue  187 GLN
Chi-restraints excluded: chain C residue  188 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  316 ASP
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:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 80 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 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 = 0.4637 r_free = 0.4637 target = 0.207921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.185373 restraints weight = 23970.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.4401 rms_B_bonded: 3.41
r_work: 0.4302 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5655
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8379  Z= 0.159
  Angle     :  0.601  15.106  11382  Z= 0.319
  Chirality :  0.095   1.671   1272
  Planarity :  0.004   0.039   1473
  Dihedral  :  5.111  38.539   1127
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 49.90
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.77 %
    Favored  : 83.93 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 23.64 %
    Favored  : 70.70 %
  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: -3.35 (0.26), residues: 1008
  helix: -0.17 (0.31), residues: 267
  sheet: -2.70 (0.37), residues: 201
  loop : -3.23 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP C 145 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.017   0.001   PHE C 397 
 TYR   0.008   0.001   TYR B 279 
 ARG   0.001   0.000   ARG A 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  307)
  hydrogen bonds       : angle       6.05675 (  849)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.78602 (    6)
  covalent geometry    : bond        0.00354 ( 8376)
  covalent geometry    : angle       0.60107 (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
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 150
  time to evaluate  : 1.103 
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  145 TRP cc_start: 0.4709 (t-100) cc_final: 0.4424 (t-100)
REVERT: A  318 ARG cc_start: 0.2700 (OUTLIER) cc_final: 0.2404 (mtm110)
REVERT: A  371 TYR cc_start: 0.7005 (m-80) cc_final: 0.6585 (m-80)
REVERT: B  108 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.1902 (ptt-90)
REVERT: B  397 PHE cc_start: 0.6567 (m-80) cc_final: 0.6174 (m-80)
REVERT: C  397 PHE cc_start: 0.6628 (m-80) cc_final: 0.6211 (m-80)
  outliers start: 52
  outliers final: 41
  residues processed: 187
  average time/residue: 0.2701
  time to fit residues: 72.6505
Evaluate side-chains
  193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 150
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  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  326 ASP
Chi-restraints excluded: chain A residue  383 LEU
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  108 ARG
Chi-restraints excluded: chain B residue  120 VAL
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  258 ILE
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 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  120 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0970
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0060
   chunk 6 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.5194

-------------------------------------------------------------------------------
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 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 = 0.4639 r_free = 0.4639 target = 0.208478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.185617 restraints weight = 24035.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.4408 rms_B_bonded: 3.46
r_work: 0.4306 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5642
moved from start:          0.1221

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= 0.137
  Angle     :  0.594  15.125  11382  Z= 0.312
  Chirality :  0.095   1.695   1272
  Planarity :  0.004   0.037   1473
  Dihedral  :  5.040  39.624   1127
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 48.36
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.08 %
    Favored  : 84.62 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 23.97 %
    Favored  : 70.04 %
  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: -3.21 (0.26), residues: 1008
  helix: -0.06 (0.31), residues: 267
  sheet: -2.35 (0.40), residues: 180
  loop : -3.26 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP C 145 
 HIS   0.003   0.001   HIS A 233 
 PHE   0.015   0.001   PHE A 205 
 TYR   0.009   0.001   TYR C 139 
 ARG   0.002   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (  307)
  hydrogen bonds       : angle       6.00497 (  849)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.88730 (    6)
  covalent geometry    : bond        0.00311 ( 8376)
  covalent geometry    : angle       0.59349 (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
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 145
  time to evaluate  : 1.127 
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: symmetry clash
REVERT: A  145 TRP cc_start: 0.4679 (t-100) cc_final: 0.4393 (t-100)
REVERT: A  318 ARG cc_start: 0.2667 (OUTLIER) cc_final: 0.2362 (mtm110)
REVERT: A  371 TYR cc_start: 0.7010 (m-80) cc_final: 0.6593 (m-80)
REVERT: B  108 ARG cc_start: 0.4501 (OUTLIER) cc_final: 0.1691 (ptt-90)
REVERT: B  111 GLN cc_start: 0.6218 (mp10) cc_final: 0.5853 (mp10)
REVERT: B  199 TYR cc_start: 0.5095 (t80) cc_final: 0.4841 (t80)
REVERT: B  390 ILE cc_start: 0.7409 (mm) cc_final: 0.7202 (mm)
REVERT: B  397 PHE cc_start: 0.6580 (m-80) cc_final: 0.6135 (m-80)
REVERT: C  108 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.1548 (ptt-90)
REVERT: C  241 THR cc_start: 0.4392 (m) cc_final: 0.4003 (m)
REVERT: C  397 PHE cc_start: 0.6591 (m-80) cc_final: 0.6162 (m-80)
  outliers start: 55
  outliers final: 46
  residues processed: 184
  average time/residue: 0.2687
  time to fit residues: 71.2928
Evaluate side-chains
  193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 144
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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  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  316 ASP
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  383 LEU
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  120 VAL
Chi-restraints excluded: chain B residue  139 TYR
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  191 ILE
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  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  120 VAL
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  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
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:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 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 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 = 0.4617 r_free = 0.4617 target = 0.206267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.183450 restraints weight = 24405.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 3.48
r_work: 0.4279 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5689
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8379  Z= 0.184
  Angle     :  0.617  15.074  11382  Z= 0.328
  Chirality :  0.095   1.662   1272
  Planarity :  0.004   0.037   1473
  Dihedral  :  5.233  39.958   1127
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 53.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.38 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 22.88 %
    Favored  : 70.26 %
  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: -3.51 (0.26), residues: 1008
  helix: -0.56 (0.30), residues: 282
  sheet: -2.83 (0.37), residues: 198
  loop : -3.22 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP C 145 
 HIS   0.003   0.001   HIS B 160 
 PHE   0.016   0.001   PHE A 205 
 TYR   0.010   0.001   TYR B 279 
 ARG   0.001   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  307)
  hydrogen bonds       : angle       5.99925 (  849)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.96775 (    6)
  covalent geometry    : bond        0.00410 ( 8376)
  covalent geometry    : angle       0.61635 (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
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 147
  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  145 TRP cc_start: 0.4783 (t-100) cc_final: 0.4459 (t-100)
REVERT: A  318 ARG cc_start: 0.2726 (OUTLIER) cc_final: 0.2355 (mtm110)
REVERT: B  108 ARG cc_start: 0.4703 (OUTLIER) cc_final: 0.1907 (ptt-90)
REVERT: B  199 TYR cc_start: 0.5187 (t80) cc_final: 0.4940 (t80)
REVERT: B  397 PHE cc_start: 0.6679 (m-80) cc_final: 0.6197 (m-80)
REVERT: C  108 ARG cc_start: 0.5226 (OUTLIER) cc_final: 0.1739 (ptt-90)
REVERT: C  397 PHE cc_start: 0.6640 (m-80) cc_final: 0.6307 (m-80)
  outliers start: 63
  outliers final: 47
  residues processed: 194
  average time/residue: 0.2949
  time to fit residues: 80.5240
Evaluate side-chains
  198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 148
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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  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  313 THR
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  383 LEU
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  187 GLN
Chi-restraints excluded: chain B residue  188 CYS
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  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  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  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:    0.7980
   chunk 5 optimal weight:    0.2980
   chunk 90 optimal weight:    0.0470
   chunk 57 optimal weight:    0.0570
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.2196

-------------------------------------------------------------------------------
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 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 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 = 0.4656 r_free = 0.4656 target = 0.210522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.188365 restraints weight = 24127.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4423 rms_B_bonded: 3.37
r_work: 0.4323 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5617
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8379  Z= 0.111
  Angle     :  0.586  15.076  11382  Z= 0.306
  Chirality :  0.095   1.675   1272
  Planarity :  0.004   0.036   1473
  Dihedral  :  5.026  40.694   1127
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 48.61
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 14.09 %
    Favored  : 85.62 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 24.51 %
    Favored  : 70.15 %
  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: -3.15 (0.26), residues: 1008
  helix:  0.05 (0.31), residues: 267
  sheet: -2.35 (0.39), residues: 180
  loop : -3.24 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 145 
 HIS   0.003   0.001   HIS A 233 
 PHE   0.012   0.001   PHE A 205 
 TYR   0.008   0.001   TYR B 279 
 ARG   0.002   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  307)
  hydrogen bonds       : angle       5.90070 (  849)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       0.97220 (    6)
  covalent geometry    : bond        0.00259 ( 8376)
  covalent geometry    : angle       0.58538 (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
  189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 140
  time to evaluate  : 0.983 
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  145 TRP cc_start: 0.4713 (t-100) cc_final: 0.4370 (t-100)
REVERT: A  318 ARG cc_start: 0.2611 (OUTLIER) cc_final: 0.2273 (mtm110)
REVERT: A  371 TYR cc_start: 0.7036 (m-80) cc_final: 0.6629 (m-80)
REVERT: B  108 ARG cc_start: 0.4428 (OUTLIER) cc_final: 0.4130 (mtt90)
REVERT: B  199 TYR cc_start: 0.5145 (t80) cc_final: 0.4886 (t80)
REVERT: B  397 PHE cc_start: 0.6671 (m-80) cc_final: 0.6182 (m-80)
REVERT: C  108 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.1434 (ptt-90)
REVERT: C  241 THR cc_start: 0.4350 (m) cc_final: 0.3935 (m)
REVERT: C  397 PHE cc_start: 0.6705 (m-80) cc_final: 0.6237 (m-80)
  outliers start: 49
  outliers final: 38
  residues processed: 175
  average time/residue: 0.2457
  time to fit residues: 62.7670
Evaluate side-chains
  181 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 140
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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  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  383 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  108 ARG
Chi-restraints excluded: chain B residue  139 TYR
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  188 CYS
Chi-restraints excluded: chain B residue  191 ILE
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  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  108 ARG
Chi-restraints excluded: chain C residue  188 CYS
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  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:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 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 = 0.4601 r_free = 0.4601 target = 0.204732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.182028 restraints weight = 24141.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.4372 rms_B_bonded: 3.43
r_work: 0.4270 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5726
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8379  Z= 0.246
  Angle     :  0.665  15.140  11382  Z= 0.355
  Chirality :  0.095   1.661   1272
  Planarity :  0.004   0.037   1473
  Dihedral  :  5.502  41.661   1127
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 58.23
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 16.27 %
    Favored  : 83.43 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 23.64 %
    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: -3.64 (0.25), residues: 1008
  helix: -0.75 (0.29), residues: 282
  sheet: -2.87 (0.37), residues: 198
  loop : -3.27 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.008   TRP C 145 
 HIS   0.007   0.001   HIS B 229 
 PHE   0.020   0.002   PHE A 205 
 TYR   0.010   0.001   TYR A 265 
 ARG   0.004   0.000   ARG C 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  307)
  hydrogen bonds       : angle       6.04251 (  849)
  SS BOND              : bond        0.00339 (    3)
  SS BOND              : angle       1.02317 (    6)
  covalent geometry    : bond        0.00539 ( 8376)
  covalent geometry    : angle       0.66436 (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
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 153
  time to evaluate  : 0.999 
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  120 VAL cc_start: 0.3205 (t) cc_final: 0.1990 (p)
REVERT: A  145 TRP cc_start: 0.4788 (t-100) cc_final: 0.4501 (t-100)
REVERT: A  197 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.4079 (mt)
REVERT: A  318 ARG cc_start: 0.2856 (OUTLIER) cc_final: 0.2435 (mtm110)
REVERT: A  397 PHE cc_start: 0.6675 (m-10) cc_final: 0.6276 (m-10)
REVERT: B  108 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.2173 (ptt-90)
REVERT: B  199 TYR cc_start: 0.5136 (t80) cc_final: 0.4918 (t80)
REVERT: B  397 PHE cc_start: 0.6738 (m-80) cc_final: 0.6243 (m-80)
REVERT: C  108 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.1848 (ptt-90)
REVERT: C  397 PHE cc_start: 0.6702 (m-80) cc_final: 0.6255 (m-80)
  outliers start: 61
  outliers final: 47
  residues processed: 197
  average time/residue: 0.3127
  time to fit residues: 83.9015
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 155
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
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  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  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  313 THR
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  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  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  373 GLN
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  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  270 ASP
Chi-restraints excluded: chain C residue  316 ASP
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  390 ILE
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:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0670
   chunk 55 optimal weight:    0.9990
   chunk 57 optimal weight:    0.3980
   chunk 67 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 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 = 0.4625 r_free = 0.4625 target = 0.206823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.184186 restraints weight = 24139.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.4395 rms_B_bonded: 3.44
r_work: 0.4293 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5686
moved from start:          0.1805

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= 0.150
  Angle     :  0.611  15.128  11382  Z= 0.322
  Chirality :  0.095   1.676   1272
  Planarity :  0.004   0.039   1473
  Dihedral  :  5.297  42.558   1127
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 51.88
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.18 %
    Favored  : 84.52 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 24.40 %
    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: -3.43 (0.26), residues: 1008
  helix: -0.53 (0.30), residues: 282
  sheet: -2.54 (0.39), residues: 177
  loop : -3.27 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP C 145 
 HIS   0.003   0.001   HIS B 229 
 PHE   0.014   0.001   PHE A 205 
 TYR   0.010   0.001   TYR C 139 
 ARG   0.002   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03349 (  307)
  hydrogen bonds       : angle       5.95269 (  849)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       1.01921 (    6)
  covalent geometry    : bond        0.00338 ( 8376)
  covalent geometry    : angle       0.61059 (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
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 148
  time to evaluate  : 1.052 
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: A  120 VAL cc_start: 0.3308 (t) cc_final: 0.2062 (p)
REVERT: A  145 TRP cc_start: 0.4778 (t-100) cc_final: 0.4469 (t-100)
REVERT: A  197 LEU cc_start: 0.4423 (OUTLIER) cc_final: 0.4177 (mt)
REVERT: A  318 ARG cc_start: 0.2799 (OUTLIER) cc_final: 0.2474 (mtm110)
REVERT: B  108 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4479 (mtt90)
REVERT: B  120 VAL cc_start: 0.2920 (t) cc_final: 0.1608 (p)
REVERT: B  397 PHE cc_start: 0.6732 (m-80) cc_final: 0.6240 (m-80)
REVERT: C  108 ARG cc_start: 0.5042 (OUTLIER) cc_final: 0.1521 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3184 (t) cc_final: 0.1803 (p)
REVERT: C  241 THR cc_start: 0.4462 (m) cc_final: 0.4087 (m)
REVERT: C  340 LYS cc_start: 0.4658 (OUTLIER) cc_final: 0.4224 (ptpp)
REVERT: C  397 PHE cc_start: 0.6776 (m-80) cc_final: 0.6309 (m-80)
  outliers start: 55
  outliers final: 48
  residues processed: 191
  average time/residue: 0.2808
  time to fit residues: 75.7081
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 148
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
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  261 THR
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  326 ASP
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  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  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  373 GLN
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0060
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 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 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 = 0.4630 r_free = 0.4630 target = 0.207443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.184751 restraints weight = 24170.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4400 rms_B_bonded: 3.44
r_work: 0.4297 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5675
moved from start:          0.1861

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= 0.141
  Angle     :  0.606  15.089  11382  Z= 0.318
  Chirality :  0.095   1.673   1272
  Planarity :  0.004   0.049   1473
  Dihedral  :  5.228  42.707   1127
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 52.43
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.67 %
    Favored  : 84.03 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 25.27 %
    Favored  : 69.17 %
  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: -3.29 (0.26), residues: 1008
  helix: -0.17 (0.31), residues: 267
  sheet: -2.43 (0.39), residues: 180
  loop : -3.28 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP C 145 
 HIS   0.003   0.001   HIS A 233 
 PHE   0.013   0.001   PHE A 205 
 TYR   0.011   0.001   TYR B 371 
 ARG   0.002   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03275 (  307)
  hydrogen bonds       : angle       5.86513 (  849)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       1.01287 (    6)
  covalent geometry    : bond        0.00319 ( 8376)
  covalent geometry    : angle       0.60568 (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
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 150
  time to evaluate  : 1.059 
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  120 VAL cc_start: 0.3257 (t) cc_final: 0.2018 (p)
REVERT: A  145 TRP cc_start: 0.4735 (t-100) cc_final: 0.4427 (t-100)
REVERT: A  197 LEU cc_start: 0.4372 (OUTLIER) cc_final: 0.4113 (mt)
REVERT: A  318 ARG cc_start: 0.2764 (OUTLIER) cc_final: 0.2437 (mtm110)
REVERT: B  108 ARG cc_start: 0.4741 (OUTLIER) cc_final: 0.4440 (mtt90)
REVERT: B  397 PHE cc_start: 0.6705 (m-80) cc_final: 0.6209 (m-80)
REVERT: C  108 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.1461 (ptt-90)
REVERT: C  120 VAL cc_start: 0.3151 (t) cc_final: 0.1762 (p)
REVERT: C  241 THR cc_start: 0.4443 (m) cc_final: 0.4068 (m)
REVERT: C  340 LYS cc_start: 0.4603 (OUTLIER) cc_final: 0.4193 (ptpp)
REVERT: C  397 PHE cc_start: 0.6771 (m-80) cc_final: 0.6291 (m-80)
  outliers start: 51
  outliers final: 46
  residues processed: 189
  average time/residue: 0.2965
  time to fit residues: 78.4251
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 148
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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  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  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  139 TYR
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  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  373 GLN
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 HIS
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4622 r_free = 0.4622 target = 0.205845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.183371 restraints weight = 24122.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.4394 rms_B_bonded: 3.42
r_work: 0.4294 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5695
moved from start:          0.1923

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= 0.167
  Angle     :  0.618  15.112  11382  Z= 0.326
  Chirality :  0.095   1.670   1272
  Planarity :  0.004   0.034   1473
  Dihedral  :  5.325  43.317   1127
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 53.42
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.58 %
    Favored  : 84.13 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 24.73 %
    Favored  : 69.17 %
  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: -3.43 (0.26), residues: 1008
  helix: -0.53 (0.30), residues: 282
  sheet: -2.56 (0.39), residues: 177
  loop : -3.26 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.006   TRP B 145 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.014   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        0.03348 (  307)
  hydrogen bonds       : angle       5.92029 (  849)
  SS BOND              : bond        0.00262 (    3)
  SS BOND              : angle       0.99423 (    6)
  covalent geometry    : bond        0.00374 ( 8376)
  covalent geometry    : angle       0.61777 (11376)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5363.83 seconds
wall clock time: 93 minutes 19.68 seconds (5599.68 seconds total)