Starting phenix.real_space_refine
on Mon Nov 17 21:32:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6av9_7007/11_2025/6av9_7007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6av9_7007/11_2025/6av9_7007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6av9_7007/11_2025/6av9_7007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6av9_7007/11_2025/6av9_7007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6av9_7007/11_2025/6av9_7007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6av9_7007/11_2025/6av9_7007.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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
     P       6      5.49       5
     S      60      5.16       5
     C    5469      2.51       5
     N    1458      2.21       5
     O    1680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8673
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 2864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2864
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 19, 'TRANS': 347}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    A, B
  Time building chain proxies: 2.39, per 1000 atoms: 0.28
  Number of scatterers: 8673
  At special positions: 0
  Unit cell: (79.116, 93.69, 135.33, 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      60     16.00
     P       6     15.00
     O    1680      8.00
     N    1458      7.00
     C    5469      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.97
  Conformation dependent library (CDL) restraints added in 346.3 milliseconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2034

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 12 sheets defined
      40.1% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'C' and resid 55 through 61
      removed outlier: 4.182A  pdb=" N   LYS C  61 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 3.640A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR C  91 " --> pdb=" O   HIS C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 122
      removed outlier: 4.048A  pdb=" N   LYS C 118 " --> pdb=" O   ALA C 114 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   THR C 120 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 146
      removed outlier: 3.809A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 181 through 194
      removed outlier: 3.771A  pdb=" N   THR C 186 " --> pdb=" O   GLY C 182 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   THR C 194 " --> pdb=" O   MET C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 205 through 216
      removed outlier: 3.555A  pdb=" N   ILE C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 232
      removed outlier: 3.726A  pdb=" N   MET C 227 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA C 228 " --> pdb=" O   GLU C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 260
      removed outlier: 3.665A  pdb=" N   THR C 260 " --> pdb=" O   ARG C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 283
      removed outlier: 3.700A  pdb=" N   THR C 278 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   TYR C 279 " --> pdb=" O   HIS C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 297
      removed outlier: 4.214A  pdb=" N   LEU C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TYR C 294 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 320
    Processing helix  chain 'C' and resid 337 through 347
      removed outlier: 3.917A  pdb=" N   GLY C 343 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 365
    Processing helix  chain 'C' and resid 366 through 371
      removed outlier: 3.736A  pdb=" N   VAL C 370 " --> pdb=" O   PRO C 367 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   HIS C 371 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 4.183A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
      removed outlier: 3.640A  pdb=" N   MET A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS A  84 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR A  91 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.048A  pdb=" N   LYS A 118 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   THR A 120 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 146
      removed outlier: 3.809A  pdb=" N   LEU A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   TYR A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 175
    Processing helix  chain 'A' and resid 181 through 194
      removed outlier: 3.771A  pdb=" N   THR A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   THR A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.556A  pdb=" N   ILE A 212 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 232
      removed outlier: 3.725A  pdb=" N   MET A 227 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 260
      removed outlier: 3.665A  pdb=" N   THR A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 283
      removed outlier: 3.700A  pdb=" N   THR A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   TYR A 279 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 297
      removed outlier: 4.214A  pdb=" N   LEU A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ALA A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 320
    Processing helix  chain 'A' and resid 337 through 347
      removed outlier: 3.916A  pdb=" N   GLY A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 365
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.736A  pdb=" N   VAL A 370 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS A 371 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 61
      removed outlier: 4.182A  pdb=" N   LYS B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 92
      removed outlier: 3.640A  pdb=" N   MET B  82 " --> pdb=" O   ASN B  78 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LYS B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR B  91 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 122
      removed outlier: 4.048A  pdb=" N   LYS B 118 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   THR B 120 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 146
      removed outlier: 3.810A  pdb=" N   LEU B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   TYR B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 175
    Processing helix  chain 'B' and resid 181 through 194
      removed outlier: 3.771A  pdb=" N   THR B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   THR B 194 " --> pdb=" O   MET B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 197
      No H-bonds generated for 'chain 'B' and resid 195 through 197'
    Processing helix  chain 'B' and resid 205 through 216
      removed outlier: 3.555A  pdb=" N   ILE B 212 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 232
      removed outlier: 3.726A  pdb=" N   MET B 227 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 260
      removed outlier: 3.666A  pdb=" N   THR B 260 " --> pdb=" O   ARG B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 283
      removed outlier: 3.700A  pdb=" N   THR B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   TYR B 279 " --> pdb=" O   HIS B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 4.214A  pdb=" N   LEU B 293 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR B 294 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ALA B 295 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 320
    Processing helix  chain 'B' and resid 337 through 347
      removed outlier: 3.917A  pdb=" N   GLY B 343 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 365
    Processing helix  chain 'B' and resid 366 through 371
      removed outlier: 3.735A  pdb=" N   VAL B 370 " --> pdb=" O   PRO B 367 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   HIS B 371 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.650A  pdb=" N   LEU C 104 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 162
      removed outlier: 3.591A  pdb=" N   THR C 160 " --> pdb=" O   LEU C 178 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 166
    Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 32
      removed outlier: 3.649A  pdb=" N   LEU A 104 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA7, first strand: chain 'A' and resid 160 through 162
      removed outlier: 3.591A  pdb=" N   THR A 160 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 166
    Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32
      removed outlier: 3.650A  pdb=" N   LEU B 104 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 162
      removed outlier: 3.591A  pdb=" N   THR B 160 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 166

    252 hydrogen bonds defined for protein.
    684 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: 1.22

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1449
        1.30 -     1.43: 2214
        1.43 -     1.55: 5085
        1.55 -     1.68: 9
        1.68 -     1.81: 108
  Bond restraints: 8865
  Sorted by residual:
  bond pdb=" CG  HIC A  73 "
       pdb=" CD2 HIC A  73 "
    ideal  model  delta    sigma   weight residual
    1.369  1.305  0.064 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" CG  HIC C  73 "
       pdb=" CD2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.369  1.307  0.062 2.00e-02 2.50e+03 9.72e+00
  bond pdb=" CG  HIC B  73 "
       pdb=" CD2 HIC B  73 "
    ideal  model  delta    sigma   weight residual
    1.369  1.307  0.062 2.00e-02 2.50e+03 9.61e+00
  bond pdb=" C   HIC B  73 "
       pdb=" O   HIC B  73 "
    ideal  model  delta    sigma   weight residual
    1.231  1.169  0.062 2.00e-02 2.50e+03 9.57e+00
  bond pdb=" C   HIC C  73 "
       pdb=" O   HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.231  1.170  0.061 2.00e-02 2.50e+03 9.40e+00
  ... (remaining 8860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 10985
        1.70 -     3.39: 816
        3.39 -     5.09: 146
        5.09 -     6.78: 56
        6.78 -     8.48: 39
  Bond angle restraints: 12042
  Sorted by residual:
  angle pdb=" N   LYS B 118 "
        pdb=" CA  LYS B 118 "
        pdb=" C   LYS B 118 "
      ideal   model   delta    sigma   weight residual
     111.82  104.11    7.71 1.16e+00 7.43e-01 4.41e+01
  angle pdb=" N   LYS C 118 "
        pdb=" CA  LYS C 118 "
        pdb=" C   LYS C 118 "
      ideal   model   delta    sigma   weight residual
     111.82  104.15    7.67 1.16e+00 7.43e-01 4.37e+01
  angle pdb=" N   LYS A 118 "
        pdb=" CA  LYS A 118 "
        pdb=" C   LYS A 118 "
      ideal   model   delta    sigma   weight residual
     111.82  104.16    7.66 1.16e+00 7.43e-01 4.36e+01
  angle pdb=" C   ALA C 131 "
        pdb=" CA  ALA C 131 "
        pdb=" CB  ALA C 131 "
      ideal   model   delta    sigma   weight residual
     115.89  108.76    7.13 1.32e+00 5.74e-01 2.92e+01
  angle pdb=" C   ALA B 131 "
        pdb=" CA  ALA B 131 "
        pdb=" CB  ALA B 131 "
      ideal   model   delta    sigma   weight residual
     115.89  108.77    7.12 1.32e+00 5.74e-01 2.91e+01
  ... (remaining 12037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.63: 5097
       21.63 -    43.26: 165
       43.26 -    64.89: 39
       64.89 -    86.53: 9
       86.53 -   108.16: 6
  Dihedral angle restraints: 5316
    sinusoidal: 2136
      harmonic: 3180
  Sorted by residual:
  dihedral pdb=" O2A ADP B 801 "
           pdb=" O3A ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" PB  ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   48.16 -108.16     1      2.00e+01 2.50e-03 3.15e+01
  dihedral pdb=" O2A ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" PB  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   48.15 -108.15     1      2.00e+01 2.50e-03 3.15e+01
  dihedral pdb=" O2A ADP C 801 "
           pdb=" O3A ADP C 801 "
           pdb=" PA  ADP C 801 "
           pdb=" PB  ADP C 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   48.14 -108.14     1      2.00e+01 2.50e-03 3.15e+01
  ... (remaining 5313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 696
       0.041 -    0.082: 421
       0.082 -    0.124: 158
       0.124 -    0.165: 43
       0.165 -    0.206: 23
  Chirality restraints: 1341
  Sorted by residual:
  chirality pdb=" CA  PHE C 223 "
            pdb=" N   PHE C 223 "
            pdb=" C   PHE C 223 "
            pdb=" CB  PHE C 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  PHE A 223 "
            pdb=" N   PHE A 223 "
            pdb=" C   PHE A 223 "
            pdb=" CB  PHE A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  PHE B 223 "
            pdb=" N   PHE B 223 "
            pdb=" C   PHE B 223 "
            pdb=" CB  PHE B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1338 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 101 "    0.051 5.00e-02 4.00e+02   7.79e-02 9.70e+00
        pdb=" N   PRO B 102 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 102 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 102 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 101 "   -0.051 5.00e-02 4.00e+02   7.78e-02 9.68e+00
        pdb=" N   PRO C 102 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO C 102 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 102 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 101 "    0.051 5.00e-02 4.00e+02   7.76e-02 9.64e+00
        pdb=" N   PRO A 102 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 123
        2.52 -     3.11: 8096
        3.11 -     3.71: 13858
        3.71 -     4.30: 19990
        4.30 -     4.90: 31022
  Nonbonded interactions: 73089
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 113 "
            pdb=" NH2 ARG A 116 "
     model   vdw
     1.920 3.200
  nonbonded pdb=" NZ  LYS C 113 "
            pdb=" NH2 ARG C 116 "
     model   vdw
     1.920 3.200
  nonbonded pdb=" NZ  LYS B 113 "
            pdb=" NH2 ARG B 116 "
     model   vdw
     1.920 3.200
  nonbonded pdb=" OG1 THR A 358 "
            pdb=" OE1 GLU A 361 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" OG1 THR C 358 "
            pdb=" OE1 GLU C 361 "
     model   vdw
     2.072 3.040
  ... (remaining 73084 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  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=0.00 max=1.00 mean=0.94
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.020
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
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      :  0.008   0.076   8865  Z= 0.371
  Angle     :  1.112   8.475  12042  Z= 0.591
  Chirality :  0.062   0.206   1341
  Planarity :  0.007   0.078   1536
  Dihedral  : 12.768 108.157   3282
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 32.31
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 12.83 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  2.93 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.62 (0.20), residues: 1068
  helix: -4.23 (0.16), residues: 300
  sheet: -2.44 (0.38), residues: 141
  loop : -2.68 (0.21), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 254 
 TYR   0.024   0.004   TYR B 337 
 PHE   0.022   0.002   PHE B 262 
 TRP   0.011   0.002   TRP C  86 
 HIS   0.007   0.003   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00812 ( 8865)
  covalent geometry    : angle       1.11208 (12042)
  hydrogen bonds       : bond        0.31873 (  252)
  hydrogen bonds       : angle      11.01604 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 247
  time to evaluate  : 0.349 
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: C  133 TYR cc_start: 0.8034 (t80) cc_final: 0.7316 (t80)
REVERT: C  325 MET cc_start: 0.9393 (ttp) cc_final: 0.9106 (mtt)
REVERT: A  315 LYS cc_start: 0.8188 (tttm) cc_final: 0.7615 (ttmm)
REVERT: B  325 MET cc_start: 0.9368 (ttp) cc_final: 0.9120 (mtt)
  outliers start: 3
  outliers final: 3
  residues processed: 250
  average time/residue: 0.0883
  time to fit residues: 31.4114
Evaluate side-chains
  143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 140
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  224 GLU
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain B residue  224 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN
C  87 HIS
C 128 ASN
C 296 ASN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  12 ASN
A  87 HIS
A 128 ASN
A 280 ASN
A 296 ASN
A 314 GLN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
B  49 GLN
B  87 HIS
B 128 ASN
B 246 GLN
B 280 ASN
B 371 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.081011 restraints weight = 24050.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.083114 restraints weight = 12019.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.084562 restraints weight = 7183.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.085451 restraints weight = 4889.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.086174 restraints weight = 3728.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8865  Z= 0.203
  Angle     :  0.881   8.205  12042  Z= 0.436
  Chirality :  0.053   0.175   1341
  Planarity :  0.006   0.062   1536
  Dihedral  : 12.378 120.546   1254
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 20.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.27 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.23), residues: 1068
  helix: -2.62 (0.22), residues: 345
  sheet: -2.37 (0.32), residues: 201
  loop : -2.21 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 254 
 TYR   0.020   0.002   TYR B 218 
 PHE   0.021   0.002   PHE C 352 
 TRP   0.012   0.002   TRP A 356 
 HIS   0.005   0.002   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8865)
  covalent geometry    : angle       0.88130 (12042)
  hydrogen bonds       : bond        0.04841 (  252)
  hydrogen bonds       : angle       6.54063 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 169
  time to evaluate  : 0.342 
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: C  123 MET cc_start: 0.8700 (mmp) cc_final: 0.8495 (mmp)
REVERT: A  354 GLN cc_start: 0.7986 (pp30) cc_final: 0.7685 (pp30)
REVERT: B  106 THR cc_start: 0.7618 (m) cc_final: 0.7308 (p)
  outliers start: 29
  outliers final: 10
  residues processed: 187
  average time/residue: 0.0764
  time to fit residues: 21.3052
Evaluate side-chains
  150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  286 ASP
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  216 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0170
   chunk 83 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 15 optimal weight:    0.4980
   chunk 18 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    2.9024

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

Flipped N/Q/H residues before XYZ refinement:
C 280 ASN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.093269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.083142 restraints weight = 23512.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.085281 restraints weight = 11904.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.086745 restraints weight = 7169.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.087757 restraints weight = 4902.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.088381 restraints weight = 3691.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8865  Z= 0.159
  Angle     :  0.832  11.733  12042  Z= 0.399
  Chirality :  0.049   0.171   1341
  Planarity :  0.005   0.055   1536
  Dihedral  : 10.697 125.922   1245
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.61 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.70 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.24), residues: 1068
  helix: -1.81 (0.24), residues: 357
  sheet: -2.06 (0.32), residues: 201
  loop : -1.85 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.018   0.002   TYR C 218 
 PHE   0.013   0.001   PHE C 352 
 TRP   0.018   0.002   TRP B 356 
 HIS   0.018   0.003   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8865)
  covalent geometry    : angle       0.83206 (12042)
  hydrogen bonds       : bond        0.03916 (  252)
  hydrogen bonds       : angle       5.68269 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.316 
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: C  119 MET cc_start: 0.8805 (tmm) cc_final: 0.8543 (tmm)
REVERT: A  119 MET cc_start: 0.8834 (tmm) cc_final: 0.8296 (tmm)
REVERT: B   34 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9107 (mp)
REVERT: B  105 LEU cc_start: 0.8748 (tp) cc_final: 0.7945 (mp)
REVERT: B  106 THR cc_start: 0.7734 (m) cc_final: 0.7315 (p)
REVERT: B  221 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8726 (tt)
REVERT: B  313 MET cc_start: 0.8457 (mtm) cc_final: 0.8066 (ttp)
  outliers start: 29
  outliers final: 18
  residues processed: 186
  average time/residue: 0.0753
  time to fit residues: 21.1853
Evaluate side-chains
  162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   88 HIS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 354 GLN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.090629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.080697 restraints weight = 24508.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.082739 restraints weight = 12241.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.084147 restraints weight = 7365.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.085084 restraints weight = 5053.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085683 restraints weight = 3840.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8865  Z= 0.203
  Angle     :  0.829   9.873  12042  Z= 0.399
  Chirality :  0.050   0.177   1341
  Planarity :  0.006   0.053   1536
  Dihedral  : 10.592 126.636   1245
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.52 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 19.22 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.24), residues: 1068
  helix: -1.57 (0.25), residues: 357
  sheet: -1.85 (0.33), residues: 207
  loop : -1.92 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 290 
 TYR   0.021   0.002   TYR B 218 
 PHE   0.014   0.002   PHE A 223 
 TRP   0.013   0.002   TRP B 356 
 HIS   0.024   0.003   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 8865)
  covalent geometry    : angle       0.82902 (12042)
  hydrogen bonds       : bond        0.03764 (  252)
  hydrogen bonds       : angle       5.59849 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 145
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  106 THR cc_start: 0.7671 (m) cc_final: 0.7424 (p)
REVERT: C  119 MET cc_start: 0.8782 (tmm) cc_final: 0.8542 (tmm)
REVERT: A   88 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7371 (m-70)
REVERT: A  119 MET cc_start: 0.8971 (tmm) cc_final: 0.8461 (tmm)
REVERT: A  313 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (ttm)
REVERT: B  313 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7914 (ttp)
  outliers start: 44
  outliers final: 17
  residues processed: 175
  average time/residue: 0.0789
  time to fit residues: 20.4760
Evaluate side-chains
  151 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  354 GLN
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0470
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 86 optimal weight:   20.0000
   chunk 80 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    3.0086

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

Flipped N/Q/H residues before XYZ refinement:
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  12 ASN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
B 354 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.093055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.082835 restraints weight = 23959.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.084985 restraints weight = 12050.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.086464 restraints weight = 7274.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.087514 restraints weight = 4971.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.088174 restraints weight = 3734.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8865  Z= 0.153
  Angle     :  0.800  10.851  12042  Z= 0.379
  Chirality :  0.048   0.197   1341
  Planarity :  0.005   0.051   1536
  Dihedral  : 10.284 128.375   1245
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.80 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 19.22 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.25), residues: 1068
  helix: -1.19 (0.26), residues: 357
  sheet: -1.68 (0.35), residues: 207
  loop : -1.83 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.020   0.001   TYR A 218 
 PHE   0.019   0.001   PHE A 223 
 TRP   0.016   0.002   TRP B 356 
 HIS   0.026   0.003   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8865)
  covalent geometry    : angle       0.80041 (12042)
  hydrogen bonds       : bond        0.03455 (  252)
  hydrogen bonds       : angle       5.36251 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 149
  time to evaluate  : 0.364 
Fit side-chains
REVERT: C  119 MET cc_start: 0.8756 (tmm) cc_final: 0.8489 (tmm)
REVERT: C  123 MET cc_start: 0.8623 (mmp) cc_final: 0.8370 (mmp)
REVERT: C  325 MET cc_start: 0.4623 (mtt) cc_final: 0.4230 (mtt)
REVERT: A   82 MET cc_start: 0.8155 (tpt) cc_final: 0.7706 (tmm)
REVERT: A   87 HIS cc_start: 0.8119 (t-90) cc_final: 0.7811 (t-90)
REVERT: A  119 MET cc_start: 0.8924 (tmm) cc_final: 0.8473 (tmm)
REVERT: A  123 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8251 (mmp)
REVERT: A  313 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8125 (ttp)
REVERT: A  324 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8362 (t)
REVERT: B   75 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9085 (tt)
REVERT: B  221 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8745 (tt)
REVERT: B  299 MET cc_start: 0.7297 (ttt) cc_final: 0.7071 (ttt)
REVERT: B  313 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7950 (ttp)
  outliers start: 46
  outliers final: 24
  residues processed: 179
  average time/residue: 0.0827
  time to fit residues: 21.7849
Evaluate side-chains
  162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   86 TRP
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   88 HIS
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0570
   chunk 97 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9980
   chunk 103 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.5700

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

Flipped N/Q/H residues before XYZ refinement:
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.095560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.085414 restraints weight = 23674.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087650 restraints weight = 11749.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.089158 restraints weight = 7011.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090167 restraints weight = 4769.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.090821 restraints weight = 3582.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8865  Z= 0.133
  Angle     :  0.790   9.735  12042  Z= 0.370
  Chirality :  0.047   0.196   1341
  Planarity :  0.005   0.048   1536
  Dihedral  :  9.964 131.376   1245
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.86 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 20.20 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.25), residues: 1068
  helix: -0.95 (0.26), residues: 357
  sheet: -1.18 (0.38), residues: 186
  loop : -1.79 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 290 
 TYR   0.018   0.001   TYR C 218 
 PHE   0.012   0.001   PHE C 352 
 TRP   0.016   0.002   TRP B 356 
 HIS   0.020   0.002   HIS C 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8865)
  covalent geometry    : angle       0.78983 (12042)
  hydrogen bonds       : bond        0.03173 (  252)
  hydrogen bonds       : angle       5.11012 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 164
  time to evaluate  : 0.358 
Fit side-chains
REVERT: C   75 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8983 (tt)
REVERT: C  305 MET cc_start: 0.8394 (mmm) cc_final: 0.7989 (mmm)
REVERT: C  314 GLN cc_start: 0.8299 (tp40) cc_final: 0.7750 (mm110)
REVERT: A   82 MET cc_start: 0.8091 (tpt) cc_final: 0.7131 (tmm)
REVERT: A   88 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7366 (m-70)
REVERT: A   89 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8673 (t)
REVERT: A  119 MET cc_start: 0.8850 (tmm) cc_final: 0.8471 (tmm)
REVERT: A  259 GLU cc_start: 0.8017 (pt0) cc_final: 0.7742 (pt0)
REVERT: A  313 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8095 (ttm)
REVERT: A  324 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8363 (t)
REVERT: B  105 LEU cc_start: 0.8361 (tp) cc_final: 0.8080 (mp)
REVERT: B  313 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8012 (ttp)
REVERT: B  354 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7942 (pp30)
  outliers start: 41
  outliers final: 19
  residues processed: 188
  average time/residue: 0.0829
  time to fit residues: 23.0417
Evaluate side-chains
  160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   88 HIS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  354 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 80 optimal weight:    6.9990
   chunk 40 optimal weight:   30.0000
   chunk 7 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9980
   chunk 103 optimal weight:    9.9990
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.095277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.085111 restraints weight = 24067.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.087286 restraints weight = 11981.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088798 restraints weight = 7203.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.089826 restraints weight = 4909.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.090439 restraints weight = 3671.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8865  Z= 0.140
  Angle     :  0.809  10.602  12042  Z= 0.380
  Chirality :  0.048   0.180   1341
  Planarity :  0.005   0.049   1536
  Dihedral  :  9.838 130.745   1245
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.39 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.06 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.25), residues: 1068
  helix: -0.94 (0.26), residues: 369
  sheet: -1.18 (0.38), residues: 183
  loop : -1.76 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.019   0.001   TYR A 218 
 PHE   0.034   0.002   PHE C 352 
 TRP   0.019   0.001   TRP C 356 
 HIS   0.026   0.002   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8865)
  covalent geometry    : angle       0.80857 (12042)
  hydrogen bonds       : bond        0.03251 (  252)
  hydrogen bonds       : angle       5.07367 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8247 (tpt) cc_final: 0.7775 (tmm)
REVERT: A   88 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7318 (m-70)
REVERT: A  119 MET cc_start: 0.8877 (tmm) cc_final: 0.8441 (tmm)
REVERT: A  313 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8003 (ttm)
REVERT: A  324 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8327 (t)
REVERT: B  354 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8072 (pp30)
  outliers start: 37
  outliers final: 24
  residues processed: 163
  average time/residue: 0.0742
  time to fit residues: 18.2018
Evaluate side-chains
  162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   88 HIS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  354 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 64 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 354 GLN
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 GLN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.091266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.081258 restraints weight = 24214.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.083332 restraints weight = 12082.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084758 restraints weight = 7254.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.085739 restraints weight = 4980.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.086338 restraints weight = 3766.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8865  Z= 0.227
  Angle     :  0.872  10.120  12042  Z= 0.416
  Chirality :  0.051   0.190   1341
  Planarity :  0.005   0.049   1536
  Dihedral  : 10.078 126.484   1245
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.42 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 21.61 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.25), residues: 1068
  helix: -1.11 (0.26), residues: 369
  sheet: -1.24 (0.38), residues: 183
  loop : -1.85 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 290 
 TYR   0.024   0.002   TYR A 218 
 PHE   0.034   0.002   PHE C 352 
 TRP   0.015   0.002   TRP C 356 
 HIS   0.025   0.003   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 8865)
  covalent geometry    : angle       0.87175 (12042)
  hydrogen bonds       : bond        0.03668 (  252)
  hydrogen bonds       : angle       5.31153 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 130
  time to evaluate  : 0.336 
Fit side-chains
REVERT: C   76 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8187 (pt)
REVERT: C  103 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8516 (p)
REVERT: A   88 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7557 (m-70)
REVERT: A  119 MET cc_start: 0.8900 (tmm) cc_final: 0.8403 (tmm)
REVERT: A  313 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8095 (ttp)
REVERT: A  324 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8320 (t)
  outliers start: 45
  outliers final: 28
  residues processed: 161
  average time/residue: 0.0745
  time to fit residues: 17.9911
Evaluate side-chains
  159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  250 ILE
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  354 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 GLN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 HIS
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.092226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.082182 restraints weight = 24221.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.084281 restraints weight = 12286.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.085726 restraints weight = 7424.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.086685 restraints weight = 5099.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.087258 restraints weight = 3870.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8865  Z= 0.188
  Angle     :  0.859  10.547  12042  Z= 0.408
  Chirality :  0.049   0.201   1341
  Planarity :  0.005   0.049   1536
  Dihedral  :  9.993 125.535   1245
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 10.96 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 22.58 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.25), residues: 1068
  helix: -1.14 (0.25), residues: 369
  sheet: -1.18 (0.39), residues: 183
  loop : -1.82 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.023   0.002   TYR A 218 
 PHE   0.036   0.002   PHE C 352 
 TRP   0.017   0.002   TRP C 356 
 HIS   0.024   0.003   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8865)
  covalent geometry    : angle       0.85864 (12042)
  hydrogen bonds       : bond        0.03497 (  252)
  hydrogen bonds       : angle       5.26149 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.304 
Fit side-chains
REVERT: C   76 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8161 (pt)
REVERT: C  176 MET cc_start: 0.8245 (mmm) cc_final: 0.7889 (mmm)
REVERT: A  119 MET cc_start: 0.8865 (tmm) cc_final: 0.8378 (tmm)
REVERT: A  299 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6172 (ptm)
REVERT: A  313 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8051 (ttm)
REVERT: A  324 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (t)
REVERT: B  119 MET cc_start: 0.8827 (tmm) cc_final: 0.8468 (tmm)
  outliers start: 40
  outliers final: 31
  residues processed: 156
  average time/residue: 0.0754
  time to fit residues: 17.6378
Evaluate side-chains
  164 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   87 HIS
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   88 HIS
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  327 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 43 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN
** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 371 HIS
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 GLN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.081350 restraints weight = 24294.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.083420 restraints weight = 12236.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084813 restraints weight = 7376.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.085757 restraints weight = 5077.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.086340 restraints weight = 3852.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8865  Z= 0.209
  Angle     :  0.883  11.095  12042  Z= 0.421
  Chirality :  0.050   0.202   1341
  Planarity :  0.005   0.049   1536
  Dihedral  : 10.027 124.120   1245
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 19.51
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 12.27 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 22.80 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.25), residues: 1068
  helix: -1.25 (0.25), residues: 369
  sheet: -1.16 (0.39), residues: 183
  loop : -1.82 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.024   0.002   TYR A 218 
 PHE   0.036   0.002   PHE C 352 
 TRP   0.016   0.002   TRP C 356 
 HIS   0.024   0.003   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 8865)
  covalent geometry    : angle       0.88254 (12042)
  hydrogen bonds       : bond        0.03624 (  252)
  hydrogen bonds       : angle       5.31976 (  684)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 126
  time to evaluate  : 0.318 
Fit side-chains
REVERT: C   76 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8126 (pt)
REVERT: C  176 MET cc_start: 0.8220 (mmm) cc_final: 0.7926 (mmm)
REVERT: A  119 MET cc_start: 0.8872 (tmm) cc_final: 0.8373 (tmm)
REVERT: A  299 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.6122 (ptm)
REVERT: A  313 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8138 (ttp)
REVERT: A  324 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (t)
REVERT: B   82 MET cc_start: 0.8163 (tpt) cc_final: 0.7737 (tmm)
REVERT: B  119 MET cc_start: 0.8722 (tmm) cc_final: 0.8402 (tmm)
REVERT: B  355 MET cc_start: 0.7772 (mmm) cc_final: 0.7353 (tpp)
  outliers start: 41
  outliers final: 33
  residues processed: 151
  average time/residue: 0.0732
  time to fit residues: 16.6815
Evaluate side-chains
  163 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 126
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   87 HIS
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   88 HIS
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 79 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 11 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 4 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 GLN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.093197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.083198 restraints weight = 24004.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.085301 restraints weight = 12195.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.086729 restraints weight = 7369.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.087672 restraints weight = 5061.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.088346 restraints weight = 3840.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8865  Z= 0.164
  Angle     :  0.848  10.537  12042  Z= 0.400
  Chirality :  0.049   0.183   1341
  Planarity :  0.005   0.050   1536
  Dihedral  :  9.847 124.416   1245
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.05 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 22.26 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.25), residues: 1068
  helix: -1.12 (0.25), residues: 369
  sheet: -1.11 (0.39), residues: 183
  loop : -1.75 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.022   0.002   TYR A 218 
 PHE   0.037   0.002   PHE C 352 
 TRP   0.019   0.002   TRP C 356 
 HIS   0.022   0.002   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8865)
  covalent geometry    : angle       0.84849 (12042)
  hydrogen bonds       : bond        0.03375 (  252)
  hydrogen bonds       : angle       5.17751 (  684)

===============================================================================
Job complete
usr+sys time: 1243.66 seconds
wall clock time: 22 minutes 25.66 seconds (1345.66 seconds total)