Starting phenix.real_space_refine
on Wed Sep 17 11:10:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zfa_60054/09_2025/8zfa_60054_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zfa_60054/09_2025/8zfa_60054.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zfa_60054/09_2025/8zfa_60054_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zfa_60054/09_2025/8zfa_60054_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zfa_60054/09_2025/8zfa_60054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zfa_60054/09_2025/8zfa_60054.map"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5272      2.51       5
     N    1453      2.21       5
     O    1535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8313
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1861
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 75
    Chain: "B"
      Number of atoms: 2483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2483
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 85
    Chain: "G"
      Number of atoms: 355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 355
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 1922
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 258}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 229
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 12, 'ASP:plan': 2, 'TYR:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 142
    Chain: "S"
      Number of atoms: 1692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1692
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 42
  Time building chain proxies: 2.14, per 1000 atoms: 0.26
  Number of scatterers: 8313
  At special positions: 0
  Unit cell: (86.92, 124.02, 125.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1535      8.00
     N    1453      7.00
     C    5272      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 418.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2106

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.8% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 39
      removed outlier: 3.810A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 243 through 249
      removed outlier: 3.844A  pdb=" N   ASN A 249 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.677A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 18 through 47
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 79
      removed outlier: 4.143A  pdb=" N   VAL R  54 " --> pdb=" O   ARG R  50 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 90 through 121
      removed outlier: 3.989A  pdb=" N   ALA R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 150
      removed outlier: 4.035A  pdb=" N   SER R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 191
      removed outlier: 4.224A  pdb=" N   VAL R 184 " --> pdb=" O   ALA R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 209
    Processing helix  chain 'R' and resid 210 through 212
      No H-bonds generated for 'chain 'R' and resid 210 through 212'
    Processing helix  chain 'R' and resid 216 through 228
      removed outlier: 3.866A  pdb=" N   ARG R 222 " --> pdb=" O   ARG R 218 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 239
    Processing helix  chain 'R' and resid 239 through 253
    Processing helix  chain 'R' and resid 264 through 283
      Proline residue:  R 273  - end of helix
      removed outlier: 3.795A  pdb=" N   ALA R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU R 279 " --> pdb=" O   TYR R 275 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   ALA R 280 " --> pdb=" O   HIS R 276 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU R 281 " --> pdb=" O   ALA R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 294
      Proline residue:  R 290  - end of helix
    Processing helix  chain 'R' and resid 297 through 307
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.848A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.647A  pdb=" N   ASP S  90 " --> pdb=" O   ARG S  87 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 87 through 91'
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.908A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224
      removed outlier: 4.900A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 9.489A  pdb=" N   ALA A 253 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   ILE A 255 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   VAL A 257 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ASP A 259 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL A 258 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.503A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.785A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.482A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.580A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.545A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.339A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.891A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.748A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.090A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.677A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)

    439 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 0.91 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: 1348
        1.30 -     1.43: 2298
        1.43 -     1.55: 4771
        1.55 -     1.68: 3
        1.68 -     1.81: 72
  Bond restraints: 8492
  Sorted by residual:
  bond pdb=" C   ARG A 385 "
       pdb=" O   ARG A 385 "
    ideal  model  delta    sigma   weight residual
    1.236  1.169  0.068 1.26e-02 6.30e+03 2.89e+01
  bond pdb=" C   SER R 171 "
       pdb=" O   SER R 171 "
    ideal  model  delta    sigma   weight residual
    1.233  1.184  0.049 1.35e-02 5.49e+03 1.30e+01
  bond pdb=" C   GLY R  88 "
       pdb=" O   GLY R  88 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.35e-02 5.49e+03 1.09e+01
  bond pdb=" CA  VAL R  82 "
       pdb=" C   VAL R  82 "
    ideal  model  delta    sigma   weight residual
    1.522  1.485  0.037 1.21e-02 6.83e+03 9.36e+00
  bond pdb=" C   THR R 166 "
       pdb=" O   THR R 166 "
    ideal  model  delta    sigma   weight residual
    1.233  1.194  0.039 1.36e-02 5.41e+03 8.23e+00
  ... (remaining 8487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 11475
        2.98 -     5.96: 79
        5.96 -     8.94: 12
        8.94 -    11.93: 2
       11.93 -    14.91: 4
  Bond angle restraints: 11572
  Sorted by residual:
  angle pdb=" N   GLU R 170 "
        pdb=" CA  GLU R 170 "
        pdb=" C   GLU R 170 "
      ideal   model   delta    sigma   weight residual
     110.48  123.76  -13.28 1.48e+00 4.57e-01 8.05e+01
  angle pdb=" N   PRO R  87 "
        pdb=" CA  PRO R  87 "
        pdb=" C   PRO R  87 "
      ideal   model   delta    sigma   weight residual
     112.47   99.30   13.17 2.06e+00 2.36e-01 4.09e+01
  angle pdb=" CA  CYS R 168 "
        pdb=" CB  CYS R 168 "
        pdb=" SG  CYS R 168 "
      ideal   model   delta    sigma   weight residual
     114.40   99.77   14.63 2.30e+00 1.89e-01 4.04e+01
  angle pdb=" N   SER R 171 "
        pdb=" CA  SER R 171 "
        pdb=" C   SER R 171 "
      ideal   model   delta    sigma   weight residual
     107.71  119.35  -11.64 1.90e+00 2.77e-01 3.75e+01
  angle pdb=" N   CYS R 168 "
        pdb=" CA  CYS R 168 "
        pdb=" C   CYS R 168 "
      ideal   model   delta    sigma   weight residual
     108.67  117.66   -8.99 1.55e+00 4.16e-01 3.36e+01
  ... (remaining 11567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4508
       16.07 -    32.15: 379
       32.15 -    48.22: 68
       48.22 -    64.30: 9
       64.30 -    80.37: 7
  Dihedral angle restraints: 4971
    sinusoidal: 1698
      harmonic: 3273
  Sorted by residual:
  dihedral pdb=" N   CYS R 168 "
           pdb=" C   CYS R 168 "
           pdb=" CA  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  145.89  -23.09     0      2.50e+00 1.60e-01 8.53e+01
  dihedral pdb=" CB  CYS R  90 "
           pdb=" SG  CYS R  90 "
           pdb=" SG  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.63  -80.37     1      1.00e+01 1.00e-02 7.99e+01
  dihedral pdb=" C   CYS R 168 "
           pdb=" N   CYS R 168 "
           pdb=" CA  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.92   22.32     0      2.50e+00 1.60e-01 7.97e+01
  ... (remaining 4968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.197: 1325
       0.197 -    0.395: 4
       0.395 -    0.592: 2
       0.592 -    0.790: 0
       0.790 -    0.987: 1
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CA  CYS R 168 "
            pdb=" N   CYS R 168 "
            pdb=" C   CYS R 168 "
            pdb=" CB  CYS R 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.52    0.99 2.00e-01 2.50e+01 2.44e+01
  chirality pdb=" CA  GLU R 170 "
            pdb=" N   GLU R 170 "
            pdb=" C   GLU R 170 "
            pdb=" CB  GLU R 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.42e+00
  chirality pdb=" CA  ASP R  81 "
            pdb=" N   ASP R  81 "
            pdb=" C   ASP R  81 "
            pdb=" CB  ASP R  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.17e+00
  ... (remaining 1329 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 169 "   -0.030 2.00e-02 2.50e+03   2.06e-02 8.45e+00
        pdb=" CG  TYR R 169 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 169 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 169 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 169 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 169 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 169 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR R 169 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 169 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.44e+00
        pdb=" C   TYR R 169 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   TYR R 169 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU R 170 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "   -0.044 5.00e-02 4.00e+02   6.72e-02 7.22e+00
        pdb=" N   PRO S  41 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 37
        2.46 -     3.07: 5398
        3.07 -     3.68: 12759
        3.68 -     4.29: 18529
        4.29 -     4.90: 31522
  Nonbonded interactions: 68245
  Sorted by model distance:
  nonbonded pdb=" O   PRO R  20 "
            pdb=" CD2 TYR R  24 "
     model   vdw
     1.845 3.340
  nonbonded pdb=" O   ASP R  81 "
            pdb=" OD1 ASP R  81 "
     model   vdw
     1.994 3.040
  nonbonded pdb=" O   ASP R  75 "
            pdb=" CG  ARG R  79 "
     model   vdw
     2.083 3.440
  nonbonded pdb=" O   LEU A   5 "
            pdb=" NZ  LYS A  10 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" NH2 ARG S  98 "
            pdb=" OD2 ASP S 109 "
     model   vdw
     2.196 3.120
  ... (remaining 68240 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.700
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.450
  Find NCS groups from input model:        0.050
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
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      :  0.004   0.068   8494  Z= 0.208
  Angle     :  0.743  14.907  11576  Z= 0.415
  Chirality :  0.058   0.987   1332
  Planarity :  0.006   0.067   1488
  Dihedral  : 12.498  75.287   2859
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  0.12 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1114
  helix:  1.44 (0.27), residues: 391
  sheet: -0.24 (0.31), residues: 268
  loop : -0.67 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R  79 
 TYR   0.048   0.001   TYR R 169 
 PHE   0.015   0.002   PHE B 234 
 TRP   0.010   0.001   TRP A 244 
 HIS   0.008   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8492)
  covalent geometry    : angle       0.73178 (11572)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       6.85176 (    4)
  hydrogen bonds       : bond        0.17164 (  434)
  hydrogen bonds       : angle       6.76189 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 205
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.6780 (m-30) cc_final: 0.6464 (m-30)
REVERT: A  219 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6528 (tm-30)
REVERT: A  289 LEU cc_start: 0.8387 (pt) cc_final: 0.8168 (pt)
REVERT: B  132 ASN cc_start: 0.7715 (p0) cc_final: 0.7413 (p0)
REVERT: B  258 ASP cc_start: 0.6228 (t0) cc_final: 0.5963 (t0)
REVERT: R   64 LEU cc_start: 0.6715 (mm) cc_final: 0.6512 (mm)
REVERT: R  116 TYR cc_start: 0.7890 (t80) cc_final: 0.7492 (t80)
REVERT: R  124 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7085 (mtt-85)
REVERT: R  193 LEU cc_start: 0.7169 (tp) cc_final: 0.6931 (tm)
REVERT: R  287 LEU cc_start: 0.7703 (tt) cc_final: 0.7464 (tp)
  outliers start: 4
  outliers final: 3
  residues processed: 209
  average time/residue: 0.5904
  time to fit residues: 130.8853
Evaluate side-chains
  173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue   81 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0270
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.1980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
B  88 ASN
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.140974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.121963 restraints weight = 12311.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.92
r_work: 0.3475 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8494  Z= 0.168
  Angle     :  0.606   6.849  11576  Z= 0.320
  Chirality :  0.044   0.132   1332
  Planarity :  0.005   0.057   1488
  Dihedral  :  5.462  76.329   1228
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  :  9.69 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1114
  helix:  1.91 (0.27), residues: 388
  sheet: -0.38 (0.31), residues: 265
  loop : -0.47 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 220 
 TYR   0.014   0.002   TYR S 173 
 PHE   0.022   0.002   PHE B 235 
 TRP   0.021   0.002   TRP B 211 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8492)
  covalent geometry    : angle       0.60609 (11572)
  SS BOND              : bond        0.00465 (    2)
  SS BOND              : angle       0.93023 (    4)
  hydrogen bonds       : bond        0.04471 (  434)
  hydrogen bonds       : angle       5.06394 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.7374 (m-30) cc_final: 0.7010 (m-30)
REVERT: A  219 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7047 (tm-30)
REVERT: A  220 THR cc_start: 0.8548 (m) cc_final: 0.7852 (t)
REVERT: A  289 LEU cc_start: 0.8514 (pt) cc_final: 0.8172 (pt)
REVERT: A  291 LEU cc_start: 0.7612 (mt) cc_final: 0.7164 (mt)
REVERT: A  347 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8139 (mtp-110)
REVERT: A  381 ASP cc_start: 0.7746 (t70) cc_final: 0.7476 (t0)
REVERT: B   59 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7260 (t80)
REVERT: B  132 ASN cc_start: 0.8040 (p0) cc_final: 0.7706 (p0)
REVERT: B  212 ASP cc_start: 0.7811 (t0) cc_final: 0.7603 (t0)
REVERT: B  219 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8207 (tpp80)
REVERT: B  258 ASP cc_start: 0.7162 (t0) cc_final: 0.6630 (t0)
REVERT: B  325 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7384 (tpp)
REVERT: B  340 ASN cc_start: 0.7134 (t0) cc_final: 0.6907 (t0)
REVERT: R  116 TYR cc_start: 0.8641 (t80) cc_final: 0.8212 (t80)
REVERT: R  124 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7797 (mtt-85)
REVERT: S   98 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7884 (ttp-170)
  outliers start: 33
  outliers final: 13
  residues processed: 184
  average time/residue: 0.5884
  time to fit residues: 115.0075
Evaluate side-chains
  185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   98 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 73 optimal weight:    0.1980
   chunk 42 optimal weight:    0.1980
   chunk 98 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0370
   overall best weight:    0.1836

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

Flipped N/Q/H residues before XYZ refinement:
B 313 ASN
S 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.143353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124608 restraints weight = 12178.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.85
r_work: 0.3517 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8494  Z= 0.115
  Angle     :  0.550   7.581  11576  Z= 0.287
  Chirality :  0.042   0.139   1332
  Planarity :  0.005   0.054   1488
  Dihedral  :  4.342  42.732   1224
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.92 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.26), residues: 1114
  helix:  2.27 (0.27), residues: 388
  sheet: -0.24 (0.30), residues: 272
  loop : -0.48 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 380 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.019   0.002   PHE R 125 
 TRP   0.019   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8492)
  covalent geometry    : angle       0.55019 (11572)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       0.35537 (    4)
  hydrogen bonds       : bond        0.03738 (  434)
  hydrogen bonds       : angle       4.60240 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.7351 (m-30) cc_final: 0.7039 (m-30)
REVERT: A  219 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7143 (tm-30)
REVERT: A  221 LYS cc_start: 0.7536 (mtmm) cc_final: 0.7208 (mtmm)
REVERT: A  223 GLN cc_start: 0.8291 (tt0) cc_final: 0.8028 (mt0)
REVERT: A  257 VAL cc_start: 0.8707 (t) cc_final: 0.8483 (t)
REVERT: A  289 LEU cc_start: 0.8509 (pt) cc_final: 0.8128 (pt)
REVERT: A  291 LEU cc_start: 0.7604 (mt) cc_final: 0.7117 (mt)
REVERT: A  338 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7375 (ptmt)
REVERT: A  381 ASP cc_start: 0.7732 (t70) cc_final: 0.7470 (t0)
REVERT: B   59 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.7335 (t80)
REVERT: B   61 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8030 (pp-130)
REVERT: B  132 ASN cc_start: 0.7873 (p0) cc_final: 0.7528 (p0)
REVERT: B  212 ASP cc_start: 0.7772 (t0) cc_final: 0.7510 (t0)
REVERT: B  219 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8171 (tpp80)
REVERT: B  258 ASP cc_start: 0.7095 (t0) cc_final: 0.6444 (t0)
REVERT: B  340 ASN cc_start: 0.7067 (t0) cc_final: 0.6828 (t0)
REVERT: R  116 TYR cc_start: 0.8654 (t80) cc_final: 0.7665 (t80)
REVERT: R  124 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7763 (mtt-85)
  outliers start: 26
  outliers final: 8
  residues processed: 179
  average time/residue: 0.5461
  time to fit residues: 103.9717
Evaluate side-chains
  180 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain S residue   86 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0570
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0470
   chunk 73 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
A 362 HIS
B  75 GLN
B 125 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.140438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.121504 restraints weight = 12379.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.95
r_work: 0.3462 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8494  Z= 0.163
  Angle     :  0.593   8.659  11576  Z= 0.311
  Chirality :  0.043   0.178   1332
  Planarity :  0.005   0.052   1488
  Dihedral  :  4.266  19.561   1222
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.53 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.26), residues: 1114
  helix:  2.22 (0.27), residues: 384
  sheet: -0.26 (0.31), residues: 271
  loop : -0.58 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 137 
 TYR   0.024   0.001   TYR R  76 
 PHE   0.022   0.002   PHE R 125 
 TRP   0.017   0.002   TRP B 211 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8492)
  covalent geometry    : angle       0.59259 (11572)
  SS BOND              : bond        0.00246 (    2)
  SS BOND              : angle       0.62779 (    4)
  hydrogen bonds       : bond        0.04175 (  434)
  hydrogen bonds       : angle       4.67069 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.7386 (m-30) cc_final: 0.7046 (m-30)
REVERT: A  221 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7353 (mtmm)
REVERT: A  289 LEU cc_start: 0.8530 (pt) cc_final: 0.8074 (pt)
REVERT: A  291 LEU cc_start: 0.7705 (mt) cc_final: 0.7161 (mt)
REVERT: A  338 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7383 (ptmt)
REVERT: A  381 ASP cc_start: 0.7791 (t70) cc_final: 0.7513 (t0)
REVERT: B   61 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8119 (pp-130)
REVERT: B   85 TYR cc_start: 0.8461 (m-10) cc_final: 0.8233 (m-10)
REVERT: B  132 ASN cc_start: 0.7966 (p0) cc_final: 0.7698 (p0)
REVERT: B  258 ASP cc_start: 0.7201 (t0) cc_final: 0.6484 (t0)
REVERT: B  325 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7492 (tpp)
REVERT: B  340 ASN cc_start: 0.7195 (t0) cc_final: 0.6929 (t0)
REVERT: R  116 TYR cc_start: 0.8653 (t80) cc_final: 0.8147 (t80)
REVERT: R  124 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7819 (mtt-85)
  outliers start: 28
  outliers final: 11
  residues processed: 181
  average time/residue: 0.5822
  time to fit residues: 112.0014
Evaluate side-chains
  182 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 168
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain S residue   86 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0270
   chunk 87 optimal weight:    0.0010
   chunk 76 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.4844

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
B 125 ASN
B 230 ASN
S 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.139699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120891 restraints weight = 12241.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.92
r_work: 0.3448 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8494  Z= 0.175
  Angle     :  0.604   7.797  11576  Z= 0.316
  Chirality :  0.044   0.193   1332
  Planarity :  0.005   0.052   1488
  Dihedral  :  4.357  19.797   1222
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 15.78 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1114
  helix:  2.13 (0.26), residues: 384
  sheet: -0.36 (0.30), residues: 271
  loop : -0.70 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 380 
 TYR   0.024   0.002   TYR R  76 
 PHE   0.024   0.002   PHE R 125 
 TRP   0.018   0.002   TRP B 211 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8492)
  covalent geometry    : angle       0.60379 (11572)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       0.58442 (    4)
  hydrogen bonds       : bond        0.04254 (  434)
  hydrogen bonds       : angle       4.70450 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.7480 (m-30) cc_final: 0.7116 (m-30)
REVERT: A   36 VAL cc_start: 0.7757 (t) cc_final: 0.7429 (p)
REVERT: A  221 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7453 (mtmm)
REVERT: A  223 GLN cc_start: 0.8351 (tt0) cc_final: 0.8105 (mt0)
REVERT: A  266 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7569 (mp)
REVERT: A  291 LEU cc_start: 0.7707 (mt) cc_final: 0.7314 (mt)
REVERT: A  338 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7375 (ptmt)
REVERT: A  347 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8152 (mtp-110)
REVERT: A  381 ASP cc_start: 0.7694 (t70) cc_final: 0.7403 (t0)
REVERT: B   61 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8143 (pp-130)
REVERT: B  134 ARG cc_start: 0.7930 (ptt-90) cc_final: 0.7671 (ptt-90)
REVERT: B  258 ASP cc_start: 0.7193 (t0) cc_final: 0.6435 (t0)
REVERT: B  325 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7446 (tpp)
REVERT: B  340 ASN cc_start: 0.7158 (t0) cc_final: 0.6873 (t0)
REVERT: R  116 TYR cc_start: 0.8644 (t80) cc_final: 0.8171 (t80)
REVERT: R  124 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7794 (mtt-85)
REVERT: R  220 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7667 (tpt90)
  outliers start: 37
  outliers final: 19
  residues processed: 189
  average time/residue: 0.5364
  time to fit residues: 107.9596
Evaluate side-chains
  193 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue  186 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.2980
   chunk 91 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0970
   chunk 69 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0470
   chunk 80 optimal weight:    0.0050
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.1290

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
B 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.143037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124641 restraints weight = 12198.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 1.85
r_work: 0.3518 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8494  Z= 0.109
  Angle     :  0.556   7.537  11576  Z= 0.287
  Chirality :  0.042   0.244   1332
  Planarity :  0.005   0.053   1488
  Dihedral  :  4.027  19.026   1222
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.14 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.26), residues: 1114
  helix:  2.43 (0.26), residues: 386
  sheet: -0.22 (0.30), residues: 272
  loop : -0.81 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 380 
 TYR   0.023   0.001   TYR R  76 
 PHE   0.021   0.001   PHE R 125 
 TRP   0.017   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8492)
  covalent geometry    : angle       0.55605 (11572)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       0.54984 (    4)
  hydrogen bonds       : bond        0.03447 (  434)
  hydrogen bonds       : angle       4.37639 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 172
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ASP cc_start: 0.7502 (m-30) cc_final: 0.7116 (m-30)
REVERT: A   36 VAL cc_start: 0.7658 (t) cc_final: 0.7307 (p)
REVERT: A  221 LYS cc_start: 0.7650 (mtmm) cc_final: 0.7405 (mtmm)
REVERT: A  289 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8039 (pt)
REVERT: A  338 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7390 (ptmt)
REVERT: B   52 ARG cc_start: 0.8052 (ptp-110) cc_final: 0.7810 (ptp90)
REVERT: B   61 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7986 (pp-130)
REVERT: B  258 ASP cc_start: 0.7153 (t0) cc_final: 0.6446 (t0)
REVERT: B  340 ASN cc_start: 0.7046 (t0) cc_final: 0.6831 (t0)
REVERT: R  116 TYR cc_start: 0.8645 (t80) cc_final: 0.7832 (t80)
REVERT: R  124 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7787 (mtt-85)
REVERT: R  220 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7470 (tpt90)
REVERT: R  236 LEU cc_start: 0.8522 (tt) cc_final: 0.8282 (tp)
  outliers start: 26
  outliers final: 10
  residues processed: 182
  average time/residue: 0.5514
  time to fit residues: 106.8714
Evaluate side-chains
  177 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 164
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   82 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 90 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN
A 230 HIS
B 125 ASN
** R 100 ASN ** 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 = 0.3819 r_free = 0.3819 target = 0.139108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.120444 restraints weight = 12266.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.90
r_work: 0.3447 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8494  Z= 0.220
  Angle     :  0.657  11.376  11576  Z= 0.337
  Chirality :  0.045   0.283   1332
  Planarity :  0.005   0.050   1488
  Dihedral  :  4.456  19.671   1222
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 18.51 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1114
  helix:  2.13 (0.26), residues: 387
  sheet: -0.23 (0.31), residues: 268
  loop : -0.86 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 380 
 TYR   0.026   0.002   TYR R  76 
 PHE   0.025   0.002   PHE R 107 
 TRP   0.018   0.002   TRP B 211 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 8492)
  covalent geometry    : angle       0.65684 (11572)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.64165 (    4)
  hydrogen bonds       : bond        0.04555 (  434)
  hydrogen bonds       : angle       4.75720 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 185
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  221 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7400 (mtmm)
REVERT: A  289 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8012 (pt)
REVERT: A  291 LEU cc_start: 0.7816 (mt) cc_final: 0.7371 (mt)
REVERT: A  338 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7468 (ptmt)
REVERT: A  381 ASP cc_start: 0.7678 (t70) cc_final: 0.7414 (t0)
REVERT: B   52 ARG cc_start: 0.7997 (ptp-110) cc_final: 0.7715 (ptp90)
REVERT: B   61 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8190 (pp-130)
REVERT: B  134 ARG cc_start: 0.7967 (ptt-90) cc_final: 0.7696 (ptt-90)
REVERT: B  143 THR cc_start: 0.8194 (m) cc_final: 0.7873 (p)
REVERT: B  186 ASP cc_start: 0.7715 (m-30) cc_final: 0.7424 (m-30)
REVERT: B  212 ASP cc_start: 0.7737 (t0) cc_final: 0.7532 (t70)
REVERT: B  255 LEU cc_start: 0.7420 (mt) cc_final: 0.7208 (mp)
REVERT: B  258 ASP cc_start: 0.7231 (t0) cc_final: 0.6432 (t0)
REVERT: B  340 ASN cc_start: 0.7144 (t0) cc_final: 0.6872 (t0)
REVERT: R  116 TYR cc_start: 0.8651 (t80) cc_final: 0.8269 (t80)
REVERT: R  124 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7841 (mtt-85)
  outliers start: 32
  outliers final: 17
  residues processed: 196
  average time/residue: 0.5695
  time to fit residues: 118.8607
Evaluate side-chains
  201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  219 GLU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 67 optimal weight:    0.1980
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 99 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.4980
   chunk 88 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
A 362 HIS
B 125 ASN
B 239 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.140104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.121502 restraints weight = 12051.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.89
r_work: 0.3464 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8494  Z= 0.180
  Angle     :  0.636  11.530  11576  Z= 0.325
  Chirality :  0.044   0.306   1332
  Planarity :  0.005   0.050   1488
  Dihedral  :  4.448  19.023   1222
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 19.13 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1114
  helix:  2.07 (0.26), residues: 387
  sheet: -0.27 (0.31), residues: 264
  loop : -0.83 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 380 
 TYR   0.027   0.002   TYR R  76 
 PHE   0.025   0.002   PHE R 125 
 TRP   0.017   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 8492)
  covalent geometry    : angle       0.63575 (11572)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       0.62972 (    4)
  hydrogen bonds       : bond        0.04254 (  434)
  hydrogen bonds       : angle       4.72035 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   36 VAL cc_start: 0.7909 (t) cc_final: 0.7620 (p)
REVERT: A  221 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7357 (mtmm)
REVERT: A  266 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7601 (mp)
REVERT: A  289 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8013 (pt)
REVERT: A  291 LEU cc_start: 0.7813 (mt) cc_final: 0.7312 (mt)
REVERT: A  338 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7414 (ptmt)
REVERT: A  347 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8158 (mtp-110)
REVERT: A  381 ASP cc_start: 0.7676 (t70) cc_final: 0.7397 (t0)
REVERT: B   61 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8150 (pp-130)
REVERT: B  134 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7749 (ptt-90)
REVERT: B  212 ASP cc_start: 0.7741 (t0) cc_final: 0.7540 (t70)
REVERT: B  258 ASP cc_start: 0.7176 (t0) cc_final: 0.6381 (t0)
REVERT: B  340 ASN cc_start: 0.7141 (t0) cc_final: 0.6884 (t0)
REVERT: R  116 TYR cc_start: 0.8676 (t80) cc_final: 0.7769 (t80)
REVERT: R  124 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7870 (mtt-85)
REVERT: R  220 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7580 (tpt90)
  outliers start: 34
  outliers final: 20
  residues processed: 188
  average time/residue: 0.5983
  time to fit residues: 119.3956
Evaluate side-chains
  199 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  219 GLU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:    0.0000
   chunk 24 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    0.3980
   chunk 107 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
B 125 ASN
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.139901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.121128 restraints weight = 12061.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.90
r_work: 0.3458 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8494  Z= 0.190
  Angle     :  0.650  12.338  11576  Z= 0.331
  Chirality :  0.045   0.319   1332
  Planarity :  0.005   0.063   1488
  Dihedral  :  4.502  18.954   1222
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 19.75 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1114
  helix:  2.04 (0.26), residues: 387
  sheet: -0.27 (0.32), residues: 264
  loop : -0.90 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 380 
 TYR   0.027   0.002   TYR R  76 
 PHE   0.025   0.002   PHE R 125 
 TRP   0.017   0.002   TRP B 211 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8492)
  covalent geometry    : angle       0.64981 (11572)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.67349 (    4)
  hydrogen bonds       : bond        0.04317 (  434)
  hydrogen bonds       : angle       4.74627 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   36 VAL cc_start: 0.7927 (t) cc_final: 0.7638 (p)
REVERT: A  221 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7375 (mtmm)
REVERT: A  266 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7621 (mp)
REVERT: A  289 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8015 (pt)
REVERT: A  291 LEU cc_start: 0.7730 (mt) cc_final: 0.7256 (mt)
REVERT: A  338 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7421 (ptmt)
REVERT: A  344 GLU cc_start: 0.7730 (tp30) cc_final: 0.7413 (mm-30)
REVERT: A  347 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7996 (mtp-110)
REVERT: A  381 ASP cc_start: 0.7662 (t70) cc_final: 0.7399 (t0)
REVERT: B   61 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8151 (pp-130)
REVERT: B  134 ARG cc_start: 0.8019 (ptt-90) cc_final: 0.7775 (ptt-90)
REVERT: B  143 THR cc_start: 0.8145 (m) cc_final: 0.7875 (p)
REVERT: B  186 ASP cc_start: 0.7688 (m-30) cc_final: 0.7422 (m-30)
REVERT: B  258 ASP cc_start: 0.7137 (t0) cc_final: 0.6346 (t0)
REVERT: B  340 ASN cc_start: 0.7151 (t0) cc_final: 0.6896 (t0)
REVERT: R  116 TYR cc_start: 0.8678 (t80) cc_final: 0.8245 (t80)
REVERT: R  124 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7862 (mtt-85)
REVERT: R  220 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7576 (tpt90)
  outliers start: 31
  outliers final: 21
  residues processed: 194
  average time/residue: 0.5476
  time to fit residues: 113.1823
Evaluate side-chains
  200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  219 GLU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 74 optimal weight:    0.2980
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0670
   chunk 71 optimal weight:    0.4980
   chunk 68 optimal weight:    0.2980
   chunk 13 optimal weight:    0.0870
   overall best weight:    0.2496

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
B 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.142153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.123457 restraints weight = 11964.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.90
r_work: 0.3489 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8494  Z= 0.129
  Angle     :  0.615  13.001  11576  Z= 0.310
  Chirality :  0.043   0.331   1332
  Planarity :  0.005   0.055   1488
  Dihedral  :  4.299  20.118   1222
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.75 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.25), residues: 1114
  helix:  2.29 (0.26), residues: 382
  sheet: -0.22 (0.31), residues: 263
  loop : -0.95 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 256 
 TYR   0.025   0.001   TYR R  76 
 PHE   0.024   0.002   PHE R 125 
 TRP   0.015   0.002   TRP B 211 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8492)
  covalent geometry    : angle       0.61528 (11572)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       0.67443 (    4)
  hydrogen bonds       : bond        0.03784 (  434)
  hydrogen bonds       : angle       4.54377 ( 1245)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.7812 (t) cc_final: 0.7495 (p)
REVERT: A  221 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7317 (mtmm)
REVERT: A  289 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8079 (pt)
REVERT: A  291 LEU cc_start: 0.7773 (mt) cc_final: 0.7243 (mt)
REVERT: A  338 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7412 (ptmt)
REVERT: A  381 ASP cc_start: 0.7619 (t70) cc_final: 0.7361 (t0)
REVERT: B   61 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8066 (pp-130)
REVERT: B  134 ARG cc_start: 0.8012 (ptt-90) cc_final: 0.7781 (ptt-90)
REVERT: B  137 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7870 (ttm-80)
REVERT: B  258 ASP cc_start: 0.7132 (t0) cc_final: 0.6330 (t0)
REVERT: B  340 ASN cc_start: 0.7095 (t0) cc_final: 0.6874 (t0)
REVERT: R  116 TYR cc_start: 0.8686 (t80) cc_final: 0.7717 (t80)
REVERT: R  124 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7837 (mtt-85)
REVERT: S   18 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6887 (tpt170)
  outliers start: 25
  outliers final: 19
  residues processed: 184
  average time/residue: 0.5509
  time to fit residues: 107.9681
Evaluate side-chains
  191 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  137 VAL
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain S residue   86 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 9 optimal weight:    0.3980
   chunk 64 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
B 125 ASN
** R 100 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.139279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.120550 restraints weight = 12051.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.89
r_work: 0.3448 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8494  Z= 0.216
  Angle     :  0.682  12.715  11576  Z= 0.347
  Chirality :  0.046   0.317   1332
  Planarity :  0.006   0.056   1488
  Dihedral  :  4.634  22.449   1222
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.50 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1114
  helix:  2.07 (0.26), residues: 384
  sheet: -0.37 (0.31), residues: 270
  loop : -0.92 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 219 
 TYR   0.028   0.002   TYR R  76 
 PHE   0.027   0.002   PHE R 125 
 TRP   0.019   0.002   TRP B 297 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8492)
  covalent geometry    : angle       0.68213 (11572)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       0.75417 (    4)
  hydrogen bonds       : bond        0.04507 (  434)
  hydrogen bonds       : angle       4.81565 ( 1245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3607.14 seconds
wall clock time: 62 minutes 7.93 seconds (3727.93 seconds total)