Starting phenix.real_space_refine
on Thu Feb 13 05:08:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6av9_7007/02_2025/6av9_7007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6av9_7007/02_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_7007/02_2025/6av9_7007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6av9_7007/02_2025/6av9_7007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6av9_7007/02_2025/6av9_7007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6av9_7007/02_2025/6av9_7007.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8673
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      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: "A"
      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:
    C, B
  Time building chain proxies: 5.17, per 1000 atoms: 0.60
  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: 2.72
  Conformation dependent library (CDL) restraints added in 944.0 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: 0.83
  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: 2.04

  Time building geometry restraints manager: 3.06 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.790
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.570
-------------------------------------------------------------------------------
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= 0.539
  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 : 32.37
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.011   0.002   TRP C  86 
 HIS   0.007   0.003   HIS A 101 
 PHE   0.022   0.002   PHE B 262 
 TYR   0.024   0.004   TYR B 337 
 ARG   0.006   0.001   ARG B 254 

*********************** 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  : 0.968 
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: 0.7321 (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: 0.7616 (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: 0.1989
  time to fit residues: 69.4275
Evaluate side-chains
  145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 142
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
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 91 optimal weight:    0.0010
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0980
   chunk 43 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0980
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  12 ASN
A  87 HIS
A 314 GLN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
B  49 GLN
B  87 HIS
** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.095721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.085658 restraints weight = 23292.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.087866 restraints weight = 11548.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.089324 restraints weight = 6875.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8865  Z= 0.215
  Angle     :  0.860   7.722  12042  Z= 0.422
  Chirality :  0.051   0.174   1341
  Planarity :  0.006   0.058   1536
  Dihedral  : 12.152 122.342   1254
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 19.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 12.16 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.22), residues: 1068
  helix: -2.31 (0.23), residues: 345
  sheet: -2.31 (0.32), residues: 204
  loop : -2.06 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 356 
 HIS   0.006   0.001   HIS B 101 
 PHE   0.023   0.002   PHE C 352 
 TYR   0.017   0.002   TYR B 218 
 ARG   0.003   0.001   ARG B 254 

*********************** 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
  234 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 208
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  105 LEU cc_start: 0.8669 (tp) cc_final: 0.8449 (mp)
REVERT: C  106 THR cc_start: 0.7723 (m) cc_final: 0.7229 (p)
REVERT: C  133 TYR cc_start: 0.7715 (t80) cc_final: 0.7314 (t80)
REVERT: C  176 MET cc_start: 0.8183 (mmm) cc_final: 0.7968 (mmm)
REVERT: C  355 MET cc_start: 0.8094 (tpt) cc_final: 0.7748 (tpp)
REVERT: A  105 LEU cc_start: 0.8459 (tp) cc_final: 0.8210 (tp)
REVERT: A  106 THR cc_start: 0.7687 (m) cc_final: 0.7478 (p)
REVERT: A  315 LYS cc_start: 0.7773 (tttm) cc_final: 0.7475 (ttmm)
REVERT: B   79 TRP cc_start: 0.8586 (m100) cc_final: 0.8167 (m100)
REVERT: B  106 THR cc_start: 0.7474 (m) cc_final: 0.7183 (p)
  outliers start: 26
  outliers final: 7
  residues processed: 225
  average time/residue: 0.1736
  time to fit residues: 56.9158
Evaluate side-chains
  163 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 156
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   95 ARG
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 2 optimal weight:    0.4980
   chunk 52 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0070
   overall best weight:    2.2802

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.095178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.084966 restraints weight = 23703.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.087158 restraints weight = 11861.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.088641 restraints weight = 7086.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8865  Z= 0.222
  Angle     :  0.821  11.521  12042  Z= 0.391
  Chirality :  0.049   0.179   1341
  Planarity :  0.005   0.050   1536
  Dihedral  : 10.465 126.586   1245
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.83 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.48 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.23), residues: 1068
  helix: -1.70 (0.25), residues: 354
  sheet: -2.09 (0.31), residues: 207
  loop : -1.85 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.017   0.002   HIS B 101 
 PHE   0.012   0.001   PHE C 352 
 TYR   0.018   0.001   TYR B 218 
 ARG   0.007   0.000   ARG B 290 

*********************** 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
  202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 173
  time to evaluate  : 1.075 
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  106 THR cc_start: 0.7695 (m) cc_final: 0.7485 (p)
REVERT: C  133 TYR cc_start: 0.7549 (t80) cc_final: 0.7271 (t80)
REVERT: A  106 THR cc_start: 0.7917 (m) cc_final: 0.7698 (p)
REVERT: A  119 MET cc_start: 0.9010 (tmm) cc_final: 0.8408 (tmm)
REVERT: A  315 LYS cc_start: 0.7968 (tttm) cc_final: 0.7440 (ttmm)
REVERT: A  324 THR cc_start: 0.8707 (p) cc_final: 0.8360 (t)
REVERT: B   34 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9041 (mp)
REVERT: B  106 THR cc_start: 0.7744 (m) cc_final: 0.7490 (p)
REVERT: B  221 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8667 (tt)
REVERT: B  313 MET cc_start: 0.8341 (mtm) cc_final: 0.7956 (ttp)
  outliers start: 29
  outliers final: 16
  residues processed: 193
  average time/residue: 0.1799
  time to fit residues: 50.3570
Evaluate side-chains
  168 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
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  216 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  286 ASP
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   95 ARG
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 30 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 72 optimal weight:   30.0000
   chunk 104 optimal weight:    6.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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**
** B  12 ASN ** 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 = 0.3314 r_free = 0.3314 target = 0.093812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.083810 restraints weight = 23735.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.085936 restraints weight = 11830.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.087363 restraints weight = 7072.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8865  Z= 0.244
  Angle     :  0.799   9.932  12042  Z= 0.381
  Chirality :  0.048   0.170   1341
  Planarity :  0.005   0.049   1536
  Dihedral  : 10.313 127.921   1245
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.39 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.76 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.24), residues: 1068
  helix: -1.40 (0.25), residues: 357
  sheet: -1.74 (0.34), residues: 201
  loop : -1.76 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 356 
 HIS   0.022   0.003   HIS B 101 
 PHE   0.011   0.002   PHE A 223 
 TYR   0.019   0.002   TYR C 218 
 ARG   0.005   0.000   ARG C 290 

*********************** 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
  197 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 160
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  313 MET cc_start: 0.8391 (mtm) cc_final: 0.8142 (ttp)
REVERT: C  324 THR cc_start: 0.8561 (p) cc_final: 0.8224 (t)
REVERT: A   82 MET cc_start: 0.8123 (tpt) cc_final: 0.7833 (tmm)
REVERT: A  119 MET cc_start: 0.8962 (tmm) cc_final: 0.8407 (tmm)
REVERT: A  313 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8113 (ttp)
REVERT: A  314 GLN cc_start: 0.8189 (tp40) cc_final: 0.7757 (mm-40)
REVERT: B  221 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8707 (tt)
REVERT: B  313 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7765 (ttp)
  outliers start: 37
  outliers final: 14
  residues processed: 183
  average time/residue: 0.1787
  time to fit residues: 47.6901
Evaluate side-chains
  153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  203 THR
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 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  221 LEU
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  327 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 105 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0370
   chunk 107 optimal weight:    2.9990
   overall best weight:    3.4066

-------------------------------------------------------------------------------
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 296 ASN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.083354 restraints weight = 23699.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.085450 restraints weight = 11855.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.086903 restraints weight = 7123.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8865  Z= 0.241
  Angle     :  0.798  10.764  12042  Z= 0.379
  Chirality :  0.048   0.194   1341
  Planarity :  0.005   0.049   1536
  Dihedral  : 10.077 125.001   1245
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.42 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 19.33 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.25), residues: 1068
  helix: -1.04 (0.26), residues: 360
  sheet: -1.76 (0.35), residues: 207
  loop : -1.85 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 356 
 HIS   0.016   0.003   HIS B 101 
 PHE   0.011   0.001   PHE C 200 
 TYR   0.019   0.002   TYR A 218 
 ARG   0.004   0.000   ARG C 290 

*********************** 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
  194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 155
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: C  107 GLU cc_start: 0.7961 (tt0) cc_final: 0.7728 (tt0)
REVERT: C  313 MET cc_start: 0.8314 (mtm) cc_final: 0.8027 (ttp)
REVERT: A  119 MET cc_start: 0.9026 (tmm) cc_final: 0.8501 (tmm)
REVERT: A  313 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8063 (ttp)
REVERT: A  324 THR cc_start: 0.8648 (p) cc_final: 0.8387 (t)
REVERT: B  283 MET cc_start: 0.8578 (mmp) cc_final: 0.8355 (mmp)
REVERT: B  313 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7758 (ttp)
  outliers start: 39
  outliers final: 20
  residues processed: 182
  average time/residue: 0.1700
  time to fit residues: 45.2588
Evaluate side-chains
  155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 VAL
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  110 LEU
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  203 THR
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  327 ILE
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   87 HIS
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  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 7 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 104 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 73 optimal weight:    8.9990
   chunk 50 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 128 ASN
** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  40 HIS
A 128 ASN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.088320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.078445 restraints weight = 24327.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.080413 restraints weight = 12356.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.081787 restraints weight = 7493.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   8865  Z= 0.447
  Angle     :  0.902   9.061  12042  Z= 0.439
  Chirality :  0.053   0.230   1341
  Planarity :  0.006   0.054   1536
  Dihedral  : 10.296 121.093   1245
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 19.87
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.89 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 18.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.24), residues: 1068
  helix: -1.29 (0.26), residues: 360
  sheet: -1.32 (0.37), residues: 186
  loop : -2.15 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 356 
 HIS   0.013   0.003   HIS B 101 
 PHE   0.012   0.002   PHE C 200 
 TYR   0.027   0.003   TYR C 294 
 ARG   0.007   0.001   ARG C 290 

*********************** 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
  191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 135
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
REVERT: C  107 GLU cc_start: 0.8129 (tt0) cc_final: 0.7900 (tt0)
REVERT: C  313 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8046 (ttp)
REVERT: C  325 MET cc_start: 0.4283 (mtt) cc_final: 0.3955 (mtt)
REVERT: A   82 MET cc_start: 0.8197 (tpt) cc_final: 0.7871 (tmm)
REVERT: A  119 MET cc_start: 0.9057 (tmm) cc_final: 0.8496 (tmm)
REVERT: A  137 GLN cc_start: 0.7976 (mm110) cc_final: 0.7744 (mp10)
REVERT: A  313 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8109 (ttp)
REVERT: B   75 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9114 (tt)
REVERT: B  313 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8093 (ttp)
REVERT: B  352 PHE cc_start: 0.7968 (t80) cc_final: 0.7735 (t80)
  outliers start: 56
  outliers final: 40
  residues processed: 170
  average time/residue: 0.1827
  time to fit residues: 45.1087
Evaluate side-chains
  166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 122
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   86 TRP
Chi-restraints excluded: chain C residue   89 THR
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  286 ASP
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  216 LEU
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   75 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  203 THR
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  309 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 55 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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  88 HIS
A  92 ASN
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 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 = 0.3277 r_free = 0.3277 target = 0.091736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.081885 restraints weight = 24005.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.083944 restraints weight = 12068.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.085373 restraints weight = 7219.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4668

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= 0.248
  Angle     :  0.812  10.669  12042  Z= 0.384
  Chirality :  0.048   0.182   1341
  Planarity :  0.005   0.054   1536
  Dihedral  :  9.892 123.958   1245
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.52 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.30 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.25), residues: 1068
  helix: -1.11 (0.26), residues: 372
  sheet: -1.12 (0.39), residues: 183
  loop : -1.99 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 356 
 HIS   0.011   0.002   HIS A  88 
 PHE   0.010   0.001   PHE C 352 
 TYR   0.021   0.002   TYR A 218 
 ARG   0.005   0.000   ARG B 290 

*********************** 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
  198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 156
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A   82 MET cc_start: 0.8128 (tpt) cc_final: 0.7794 (tmm)
REVERT: A  119 MET cc_start: 0.8981 (tmm) cc_final: 0.8428 (tmm)
REVERT: A  324 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8398 (t)
REVERT: B  313 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7995 (ttp)
  outliers start: 42
  outliers final: 32
  residues processed: 176
  average time/residue: 0.1784
  time to fit residues: 45.1464
Evaluate side-chains
  166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   86 TRP
Chi-restraints excluded: chain C residue   89 THR
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  283 MET
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   92 ASN
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  299 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   76 ILE
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue   95 ARG
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  313 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 86 optimal weight:   20.0000
   chunk 67 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.088452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.078582 restraints weight = 24661.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.080572 restraints weight = 12414.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.081965 restraints weight = 7478.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   8865  Z= 0.412
  Angle     :  0.902   9.911  12042  Z= 0.437
  Chirality :  0.052   0.190   1341
  Planarity :  0.006   0.054   1536
  Dihedral  : 10.163 123.964   1245
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 20.66
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 12.36 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 19.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.24), residues: 1068
  helix: -1.38 (0.25), residues: 369
  sheet: -1.24 (0.38), residues: 183
  loop : -2.12 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.029   0.004   HIS A 101 
 PHE   0.032   0.003   PHE B 352 
 TYR   0.025   0.003   TYR A 218 
 ARG   0.006   0.001   ARG A 290 

*********************** 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
  177 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 127
  time to evaluate  : 0.945 
Fit side-chains
REVERT: C   82 MET cc_start: 0.8391 (tpt) cc_final: 0.8181 (tmm)
REVERT: A  119 MET cc_start: 0.8991 (tmm) cc_final: 0.8457 (tmm)
REVERT: A  313 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8140 (mtm)
REVERT: B  313 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8009 (ttp)
REVERT: B  355 MET cc_start: 0.7980 (mmm) cc_final: 0.7760 (tpt)
  outliers start: 50
  outliers final: 38
  residues processed: 159
  average time/residue: 0.1809
  time to fit residues: 42.1201
Evaluate side-chains
  160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 120
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   86 TRP
Chi-restraints excluded: chain C residue   89 THR
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 C residue  250 ILE
Chi-restraints excluded: chain C residue  283 MET
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   45 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   89 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  216 LEU
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   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  203 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  327 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 105 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.094544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.084619 restraints weight = 23823.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.086741 restraints weight = 11885.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.088179 restraints weight = 7091.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.5160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8865  Z= 0.207
  Angle     :  0.825  10.129  12042  Z= 0.388
  Chirality :  0.047   0.185   1341
  Planarity :  0.005   0.053   1536
  Dihedral  :  9.713 127.414   1245
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 10.58 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 20.96 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.25), residues: 1068
  helix: -0.92 (0.26), residues: 366
  sheet: -1.28 (0.39), residues: 186
  loop : -1.91 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 356 
 HIS   0.024   0.002   HIS A 101 
 PHE   0.038   0.002   PHE B 352 
 TYR   0.019   0.001   TYR A 218 
 ARG   0.003   0.000   ARG A 290 

*********************** 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
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 160
  time to evaluate  : 0.971 
Fit side-chains
REVERT: C  176 MET cc_start: 0.8099 (mmm) cc_final: 0.7728 (mmm)
REVERT: C  300 SER cc_start: 0.8368 (p) cc_final: 0.8097 (p)
REVERT: C  325 MET cc_start: 0.3959 (mtt) cc_final: 0.3692 (mtt)
REVERT: A  119 MET cc_start: 0.8854 (tmm) cc_final: 0.8313 (tmm)
REVERT: A  324 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8373 (t)
REVERT: B   82 MET cc_start: 0.8379 (tpt) cc_final: 0.7929 (tmm)
REVERT: B  137 GLN cc_start: 0.8397 (mp10) cc_final: 0.8127 (mp10)
  outliers start: 39
  outliers final: 27
  residues processed: 179
  average time/residue: 0.1695
  time to fit residues: 44.1375
Evaluate side-chains
  169 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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  110 LEU
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  283 MET
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 77 optimal weight:    0.2980
   chunk 99 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 101 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    2.6588

-------------------------------------------------------------------------------
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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.084044 restraints weight = 24103.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086199 restraints weight = 12014.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.087654 restraints weight = 7212.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.5255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8865  Z= 0.245
  Angle     :  0.858   9.824  12042  Z= 0.403
  Chirality :  0.049   0.284   1341
  Planarity :  0.005   0.054   1536
  Dihedral  :  9.718 126.180   1245
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.11 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.26 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.25), residues: 1068
  helix: -0.84 (0.26), residues: 372
  sheet: -1.28 (0.39), residues: 186
  loop : -1.86 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 356 
 HIS   0.022   0.002   HIS A 101 
 PHE   0.040   0.002   PHE B 352 
 TYR   0.023   0.002   TYR C 218 
 ARG   0.003   0.000   ARG A 290 

********************** 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
  176 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 0.976 
Fit side-chains
REVERT: C  176 MET cc_start: 0.8093 (mmm) cc_final: 0.7698 (mmm)
REVERT: C  299 MET cc_start: 0.7562 (tpp) cc_final: 0.7205 (tpp)
REVERT: A  119 MET cc_start: 0.8820 (tmm) cc_final: 0.8314 (tmm)
REVERT: A  324 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8372 (t)
  outliers start: 31
  outliers final: 26
  residues processed: 159
  average time/residue: 0.1799
  time to fit residues: 42.2784
Evaluate side-chains
  161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 VAL
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  163 VAL
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  283 MET
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  260 THR
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 85 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 95 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0870
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.1964

-------------------------------------------------------------------------------
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  88 HIS
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 HIS
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.095248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085338 restraints weight = 23991.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.087493 restraints weight = 11944.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.088860 restraints weight = 7133.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.5413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8865  Z= 0.229
  Angle     :  0.861  10.682  12042  Z= 0.405
  Chirality :  0.049   0.251   1341
  Planarity :  0.005   0.053   1536
  Dihedral  :  9.627 124.731   1245
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 10.58 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.37 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.25), residues: 1068
  helix: -0.73 (0.26), residues: 372
  sheet: -1.21 (0.38), residues: 186
  loop : -1.75 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 356 
 HIS   0.020   0.002   HIS A 101 
 PHE   0.040   0.002   PHE B 352 
 TYR   0.021   0.001   TYR C 218 
 ARG   0.004   0.000   ARG A 290 

===============================================================================
Job complete
usr+sys time: 2258.24 seconds
wall clock time: 41 minutes 40.95 seconds (2500.95 seconds total)