Starting phenix.real_space_refine
on Sun Apr  5 04:21:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m0j_63545/04_2026/9m0j_63545_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m0j_63545/04_2026/9m0j_63545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m0j_63545/04_2026/9m0j_63545_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m0j_63545/04_2026/9m0j_63545_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m0j_63545/04_2026/9m0j_63545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m0j_63545/04_2026/9m0j_63545.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.005 sd=   0.087
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 26 atoms to isotropic.
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      51      5.16       5
     C    5160      2.51       5
     N    1399      2.21       5
     O    1504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8114
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1908
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2592
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 407
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2208
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 9, 'TRANS': 266}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'ODN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.89, per 1000 atoms: 0.23
  Number of scatterers: 8114
  At special positions: 0
  Unit cell: (93.44, 83.95, 120.45, 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      51     16.00
     O    1504      8.00
     N    1399      7.00
     C    5160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 0.75
  Conformation dependent library (CDL) restraints added in 323.8 milliseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1944

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      42.1% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.561A  pdb=" N   GLN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 229 through 245
      removed outlier: 4.014A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 298 through 318
    Processing helix  chain 'A' and resid 338 through 358
      removed outlier: 3.584A  pdb=" N   ILE A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 30
      removed outlier: 3.574A  pdb=" N   CYS B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 40
      removed outlier: 3.599A  pdb=" N   ILE B  38 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 44
      removed outlier: 3.690A  pdb=" N   TYR G  39 " --> pdb=" O   ASP G  35 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   CYS G  40 " --> pdb=" O   LEU G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 50 through 75
    Processing helix  chain 'R' and resid 82 through 108
      removed outlier: 3.603A  pdb=" N   ILE R  86 " --> pdb=" O   PRO R  82 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL R 101 " --> pdb=" O   LEU R  97 " (cutoff:3.500A)
      Proline residue:  R 102  - end of helix
      removed outlier: 3.806A  pdb=" N   TYR R 108 " --> pdb=" O   ASP R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 116 through 150
    Processing helix  chain 'R' and resid 160 through 180
    Processing helix  chain 'R' and resid 181 through 184
    Processing helix  chain 'R' and resid 212 through 226
      removed outlier: 3.723A  pdb=" N   SER R 218 " --> pdb=" O   GLN R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 226 through 251
      removed outlier: 3.730A  pdb=" N   LEU R 249 " --> pdb=" O   TYR R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 258 through 298
      removed outlier: 4.142A  pdb=" N   GLN R 262 " --> pdb=" O   HIS R 258 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL R 277 " --> pdb=" O   VAL R 273 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
    Processing helix  chain 'R' and resid 304 through 334
      removed outlier: 4.151A  pdb=" N   ILE R 310 " --> pdb=" O   ALA R 306 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASN R 322 " --> pdb=" O   LEU R 318 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   SER R 323 " --> pdb=" O   ALA R 319 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   CYS R 324 " --> pdb=" O   PHE R 320 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASN R 326 " --> pdb=" O   ASN R 322 " (cutoff:3.500A)
      Proline residue:  R 327  - end of helix
    Processing helix  chain 'R' and resid 335 through 349
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.391A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR A 327 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.943A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG B  54 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.753A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL B  76 " --> pdb=" O   HIS B  67 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER B  79 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.725A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 3.808A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.399A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS B 214 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 3.501A  pdb=" N   ARG B 256 " --> pdb=" O   THR B 248 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASP B 259 " --> pdb=" O   GLN B 264 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.827A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TYR B 294 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ASN B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   CYS B 299 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   VAL B 312 " --> pdb=" O   CYS B 299 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL B 301 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.733A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU N  81 " --> pdb=" O   LEU N  20 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.653A  pdb=" N   GLY N  10 " --> pdb=" O   GLN N 123 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 122 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA N  92 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    406 hydrogen bonds defined for protein.
    1164 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: 0.97 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2057
        1.33 -     1.45: 1568
        1.45 -     1.57: 4582
        1.57 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 8276
  Sorted by residual:
  bond pdb=" CA  PHE R 309 "
       pdb=" C   PHE R 309 "
    ideal  model  delta    sigma   weight residual
    1.524  1.474  0.050 1.26e-02 6.30e+03 1.55e+01
  bond pdb=" CA  GLN R 214 "
       pdb=" C   GLN R 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.050 1.41e-02 5.03e+03 1.25e+01
  bond pdb=" N   GLU R 215 "
       pdb=" CA  GLU R 215 "
    ideal  model  delta    sigma   weight residual
    1.458  1.418  0.040 1.28e-02 6.10e+03 9.56e+00
  bond pdb=" C   PHE R 309 "
       pdb=" N   ILE R 310 "
    ideal  model  delta    sigma   weight residual
    1.335  1.298  0.037 1.26e-02 6.30e+03 8.58e+00
  bond pdb=" CA  PHE R 309 "
       pdb=" CB  PHE R 309 "
    ideal  model  delta    sigma   weight residual
    1.529  1.483  0.046 1.58e-02 4.01e+03 8.52e+00
  ... (remaining 8271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 11102
        1.77 -     3.53: 94
        3.53 -     5.30: 18
        5.30 -     7.06: 2
        7.06 -     8.83: 1
  Bond angle restraints: 11217
  Sorted by residual:
  angle pdb=" N   GLU R 215 "
        pdb=" CA  GLU R 215 "
        pdb=" C   GLU R 215 "
      ideal   model   delta    sigma   weight residual
     112.45  103.62    8.83 1.39e+00 5.18e-01 4.03e+01
  angle pdb=" N   PHE R 115 "
        pdb=" CA  PHE R 115 "
        pdb=" C   PHE R 115 "
      ideal   model   delta    sigma   weight residual
     108.52  115.00   -6.48 1.74e+00 3.30e-01 1.39e+01
  angle pdb=" N   GLU R 111 "
        pdb=" CA  GLU R 111 "
        pdb=" C   GLU R 111 "
      ideal   model   delta    sigma   weight residual
     109.85  104.73    5.12 1.58e+00 4.01e-01 1.05e+01
  angle pdb=" N   VAL N 110 "
        pdb=" CA  VAL N 110 "
        pdb=" C   VAL N 110 "
      ideal   model   delta    sigma   weight residual
     112.29  109.57    2.72 9.40e-01 1.13e+00 8.37e+00
  angle pdb=" C   THR R  80 "
        pdb=" N   VAL R  81 "
        pdb=" CA  VAL R  81 "
      ideal   model   delta    sigma   weight residual
     120.33  122.55   -2.22 8.00e-01 1.56e+00 7.68e+00
  ... (remaining 11212 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.73: 4947
       24.73 -    49.46: 62
       49.46 -    74.19: 10
       74.19 -    98.92: 5
       98.92 -   123.65: 1
  Dihedral angle restraints: 5025
    sinusoidal: 2026
      harmonic: 2999
  Sorted by residual:
  dihedral pdb=" C   ODN R 401 "
           pdb=" C1  ODN R 401 "
           pdb=" C2  ODN R 401 "
           pdb=" C3  ODN R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.54   63.11 -123.65     1      3.00e+01 1.11e-03 1.66e+01
  dihedral pdb=" C2  ODN R 401 "
           pdb=" C   ODN R 401 "
           pdb=" C1  ODN R 401 "
           pdb=" C7  ODN R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -53.57   34.98  -88.55     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" O   ODN R 401 "
           pdb=" C   ODN R 401 "
           pdb=" C1  ODN R 401 "
           pdb=" C2  ODN R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     176.40   87.92   88.48     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 5022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1186
       0.074 -    0.147: 95
       0.147 -    0.221: 4
       0.221 -    0.294: 2
       0.294 -    0.368: 1
  Chirality restraints: 1288
  Sorted by residual:
  chirality pdb=" C19 ODN R 401 "
            pdb=" C18 ODN R 401 "
            pdb=" C6  ODN R 401 "
            pdb=" O5  ODN R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.17    2.54   -0.37 2.00e-01 2.50e+01 3.39e+00
  chirality pdb=" CA  GLN R 214 "
            pdb=" N   GLN R 214 "
            pdb=" C   GLN R 214 "
            pdb=" CB  GLN R 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ARG R 127 "
            pdb=" N   ARG R 127 "
            pdb=" C   ARG R 127 "
            pdb=" CB  ARG R 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1285 not shown)

  Planarity restraints: 1413
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 212 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   LEU R 212 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LEU R 212 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU R 213 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS R 308 "    0.006 2.00e-02 2.50e+03   1.31e-02 1.71e+00
        pdb=" C   HIS R 308 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   HIS R 308 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE R 309 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 309 "   -0.012 2.00e-02 2.50e+03   8.65e-03 1.31e+00
        pdb=" CG  PHE R 309 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 309 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 309 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 309 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 309 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 309 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1410 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 116
        2.62 -     3.19: 7645
        3.19 -     3.76: 12479
        3.76 -     4.33: 17435
        4.33 -     4.90: 29283
  Nonbonded interactions: 66958
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  79 "
            pdb=" OD1 ASP B  81 "
     model   vdw
     2.044 3.040
  nonbonded pdb=" OE2 GLU A 207 "
            pdb=" NH1 ARG A 209 "
     model   vdw
     2.121 3.120
  nonbonded pdb=" OG  SER G  56 "
            pdb=" OE1 GLU G  57 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OD1 ASN A 216 "
            pdb=" NZ  LYS B  62 "
     model   vdw
     2.137 3.120
  nonbonded pdb=" OG1 THR R  80 "
            pdb=" OD1 ASN R  83 "
     model   vdw
     2.141 3.040
  ... (remaining 66953 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.990
  Find NCS groups from input model:        0.030
  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:8.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4964
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8278  Z= 0.177
  Angle     :  0.472   8.827  11221  Z= 0.288
  Chirality :  0.042   0.368   1288
  Planarity :  0.002   0.023   1413
  Dihedral  :  9.280 123.646   3075
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  3.05 %
    Favored  : 96.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.25), residues: 1012
  helix:  0.87 (0.25), residues: 399
  sheet: -0.84 (0.34), residues: 222
  loop : -1.88 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 323 
 TYR   0.005   0.001   TYR N  95 
 PHE   0.018   0.001   PHE R 309 
 TRP   0.004   0.000   TRP A 248 
 HIS   0.007   0.001   HIS R 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8276)
  covalent geometry    : angle       0.47240 (11217)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.47305 (    4)
  hydrogen bonds       : bond        0.17345 (  406)
  hydrogen bonds       : angle       6.33143 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 213
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ARG cc_start: 0.5837 (ptp90) cc_final: 0.5263 (ptm160)
REVERT: A  257 PHE cc_start: 0.6447 (m-10) cc_final: 0.6205 (m-80)
REVERT: A  345 ASP cc_start: 0.5665 (m-30) cc_final: 0.5165 (m-30)
REVERT: N   80 TYR cc_start: 0.5859 (m-80) cc_final: 0.5314 (m-80)
REVERT: R  223 LEU cc_start: 0.8416 (tm) cc_final: 0.8196 (tt)
  outliers start: 5
  outliers final: 0
  residues processed: 218
  average time/residue: 0.5195
  time to fit residues: 120.7334
Evaluate side-chains
  113 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 234 GLN
A 324 HIS
A 352 GLN
B  59 HIS
B  93 ASN
B 147 HIS
B 271 HIS
B 300 ASN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  43 HIS
N  84 ASN
R  83 ASN
R 287 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.220997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180955 restraints weight = 8967.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4111 rms_B_bonded: 1.82
r_work: 0.3918 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3782 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   8278  Z= 0.266
  Angle     :  0.814   9.785  11221  Z= 0.427
  Chirality :  0.051   0.207   1288
  Planarity :  0.007   0.096   1413
  Dihedral  :  5.060  19.586   1204
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 13.67 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.26), residues: 1012
  helix:  1.36 (0.25), residues: 399
  sheet: -0.60 (0.35), residues: 196
  loop : -1.35 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 309 
 TYR   0.026   0.003   TYR A 327 
 PHE   0.021   0.003   PHE R 341 
 TRP   0.031   0.003   TRP R 172 
 HIS   0.008   0.003   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 8276)
  covalent geometry    : angle       0.81205 (11217)
  SS BOND              : bond        0.00450 (    2)
  SS BOND              : angle       2.84219 (    4)
  hydrogen bonds       : bond        0.05160 (  406)
  hydrogen bonds       : angle       5.10741 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6505 (ptp) cc_final: 0.6048 (ptm)
REVERT: A  200 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6985 (p0)
REVERT: B  274 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6408 (pp)
REVERT: B  309 ARG cc_start: 0.5632 (OUTLIER) cc_final: 0.4098 (mtp85)
REVERT: B  330 MET cc_start: 0.5582 (tpp) cc_final: 0.4330 (ttp)
REVERT: N   29 PHE cc_start: 0.4039 (t80) cc_final: 0.3278 (t80)
REVERT: N   34 MET cc_start: 0.6368 (mmm) cc_final: 0.5948 (mmm)
REVERT: N  106 ASP cc_start: 0.5262 (t0) cc_final: 0.4395 (m-30)
REVERT: R   78 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.5224 (ptp)
REVERT: R  328 PHE cc_start: 0.6235 (m-80) cc_final: 0.4543 (t80)
REVERT: R  332 TRP cc_start: 0.6689 (t60) cc_final: 0.6392 (t60)
  outliers start: 39
  outliers final: 18
  residues processed: 168
  average time/residue: 0.4244
  time to fit residues: 77.2287
Evaluate side-chains
  132 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain R residue   78 MET
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain R residue  296 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0970
   chunk 4 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0970
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.5976

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.223165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.183495 restraints weight = 8848.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 1.86
r_work: 0.3947 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3811 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6279
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8278  Z= 0.120
  Angle     :  0.598   8.382  11221  Z= 0.308
  Chirality :  0.042   0.166   1288
  Planarity :  0.004   0.046   1413
  Dihedral  :  4.211  17.610   1204
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.74 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.26), residues: 1012
  helix:  2.05 (0.26), residues: 395
  sheet: -0.62 (0.35), residues: 188
  loop : -1.19 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  53 
 TYR   0.022   0.001   TYR R  54 
 PHE   0.017   0.002   PHE R 341 
 TRP   0.015   0.001   TRP R 172 
 HIS   0.008   0.002   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8276)
  covalent geometry    : angle       0.59640 (11217)
  SS BOND              : bond        0.00560 (    2)
  SS BOND              : angle       2.58390 (    4)
  hydrogen bonds       : bond        0.03762 (  406)
  hydrogen bonds       : angle       4.49842 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6385 (ptp) cc_final: 0.5933 (ptm)
REVERT: A   42 ASP cc_start: 0.6163 (p0) cc_final: 0.5488 (m-30)
REVERT: A  200 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6792 (p0)
REVERT: B  274 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6698 (pp)
REVERT: B  330 MET cc_start: 0.5682 (tpp) cc_final: 0.4265 (ttp)
REVERT: N   29 PHE cc_start: 0.4171 (t80) cc_final: 0.3471 (t80)
REVERT: N   34 MET cc_start: 0.6357 (mmm) cc_final: 0.6002 (mmm)
REVERT: R  154 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5832 (mp0)
REVERT: R  215 GLU cc_start: 0.7035 (tp30) cc_final: 0.6623 (tp30)
REVERT: R  293 TYR cc_start: 0.7290 (t80) cc_final: 0.7088 (t80)
REVERT: R  328 PHE cc_start: 0.6163 (m-80) cc_final: 0.4483 (t80)
  outliers start: 30
  outliers final: 10
  residues processed: 149
  average time/residue: 0.4486
  time to fit residues: 72.0791
Evaluate side-chains
  117 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain R residue  115 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    0.0170
   chunk 4 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 87 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.1424

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 288 HIS
** R 308 HIS ** 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 = 0.4505 r_free = 0.4505 target = 0.222397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.183190 restraints weight = 9076.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 1.85
r_work: 0.3938 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3803 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.4856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8278  Z= 0.130
  Angle     :  0.600  11.710  11221  Z= 0.309
  Chirality :  0.043   0.164   1288
  Planarity :  0.004   0.045   1413
  Dihedral  :  4.232  18.854   1204
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 16.72 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.27), residues: 1012
  helix:  2.21 (0.26), residues: 395
  sheet: -0.58 (0.35), residues: 197
  loop : -1.00 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 284 
 TYR   0.024   0.002   TYR R  54 
 PHE   0.015   0.002   PHE R 341 
 TRP   0.022   0.001   TRP R 172 
 HIS   0.008   0.002   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8276)
  covalent geometry    : angle       0.59727 (11217)
  SS BOND              : bond        0.00861 (    2)
  SS BOND              : angle       2.99232 (    4)
  hydrogen bonds       : bond        0.03662 (  406)
  hydrogen bonds       : angle       4.43587 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 120
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6368 (ptp) cc_final: 0.5933 (ptm)
REVERT: A   42 ASP cc_start: 0.6315 (p0) cc_final: 0.5218 (m-30)
REVERT: A  235 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5871 (tp30)
REVERT: B  330 MET cc_start: 0.5743 (tpp) cc_final: 0.4646 (ttp)
REVERT: N   29 PHE cc_start: 0.4321 (t80) cc_final: 0.3789 (t80)
REVERT: N   34 MET cc_start: 0.6343 (mmm) cc_final: 0.5895 (mmm)
REVERT: R   78 MET cc_start: 0.5464 (ptp) cc_final: 0.5222 (ptp)
REVERT: R  154 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5831 (mp0)
REVERT: R  215 GLU cc_start: 0.7126 (tp30) cc_final: 0.6730 (tp30)
REVERT: R  263 ILE cc_start: 0.8076 (pp) cc_final: 0.7764 (tt)
REVERT: R  328 PHE cc_start: 0.6256 (m-80) cc_final: 0.4496 (t80)
  outliers start: 43
  outliers final: 21
  residues processed: 150
  average time/residue: 0.4218
  time to fit residues: 68.5305
Evaluate side-chains
  131 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  290 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 6 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 95 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  83 ASN
** R 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.221339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.181518 restraints weight = 9024.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 1.88
r_work: 0.3911 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6377
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8278  Z= 0.138
  Angle     :  0.609  10.318  11221  Z= 0.314
  Chirality :  0.043   0.157   1288
  Planarity :  0.004   0.044   1413
  Dihedral  :  4.402  18.941   1204
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 16.84 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1012
  helix:  2.18 (0.26), residues: 398
  sheet: -0.75 (0.36), residues: 191
  loop : -1.07 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 300 
 TYR   0.025   0.002   TYR R  54 
 PHE   0.020   0.002   PHE A 257 
 TRP   0.027   0.002   TRP R 172 
 HIS   0.008   0.002   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8276)
  covalent geometry    : angle       0.60564 (11217)
  SS BOND              : bond        0.00888 (    2)
  SS BOND              : angle       3.27949 (    4)
  hydrogen bonds       : bond        0.03703 (  406)
  hydrogen bonds       : angle       4.45769 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 116
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6325 (ptp) cc_final: 0.5918 (ptm)
REVERT: A   42 ASP cc_start: 0.6546 (p0) cc_final: 0.5384 (m-30)
REVERT: A  235 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5934 (tp30)
REVERT: B  274 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6749 (pp)
REVERT: B  330 MET cc_start: 0.5843 (tpp) cc_final: 0.4696 (ttp)
REVERT: N   29 PHE cc_start: 0.4402 (t80) cc_final: 0.3855 (t80)
REVERT: N   34 MET cc_start: 0.6379 (mmm) cc_final: 0.5948 (mmm)
REVERT: R  154 GLU cc_start: 0.6298 (mt-10) cc_final: 0.5803 (mp0)
REVERT: R  215 GLU cc_start: 0.7163 (tp30) cc_final: 0.6859 (tp30)
REVERT: R  263 ILE cc_start: 0.8166 (pp) cc_final: 0.7844 (tt)
REVERT: R  293 TYR cc_start: 0.7384 (t80) cc_final: 0.7164 (t80)
REVERT: R  328 PHE cc_start: 0.6390 (m-80) cc_final: 0.4527 (t80)
  outliers start: 46
  outliers final: 24
  residues processed: 149
  average time/residue: 0.4107
  time to fit residues: 66.2760
Evaluate side-chains
  133 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain R residue   83 ASN
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  213 LEU
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  290 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 78 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0870
   overall best weight:    1.3362

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

Flipped N/Q/H residues before XYZ refinement:
B  59 HIS
R  83 ASN
** R 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 322 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 = 0.4495 r_free = 0.4495 target = 0.221247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.181899 restraints weight = 8953.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.4115 rms_B_bonded: 1.79
r_work: 0.3923 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.5502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8278  Z= 0.139
  Angle     :  0.615   9.919  11221  Z= 0.317
  Chirality :  0.043   0.182   1288
  Planarity :  0.004   0.043   1413
  Dihedral  :  4.449  19.156   1204
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 18.98 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.26), residues: 1012
  helix:  2.20 (0.26), residues: 395
  sheet: -0.77 (0.35), residues: 191
  loop : -1.09 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  32 
 TYR   0.025   0.002   TYR R  54 
 PHE   0.014   0.002   PHE A 257 
 TRP   0.027   0.002   TRP R 172 
 HIS   0.008   0.002   HIS R 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8276)
  covalent geometry    : angle       0.61300 (11217)
  SS BOND              : bond        0.00042 (    2)
  SS BOND              : angle       2.93659 (    4)
  hydrogen bonds       : bond        0.03654 (  406)
  hydrogen bonds       : angle       4.46275 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 115
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.6322 (ptp) cc_final: 0.5938 (ptm)
REVERT: A  235 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5933 (tp30)
REVERT: B  274 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6845 (pp)
REVERT: B  330 MET cc_start: 0.5841 (tpp) cc_final: 0.4663 (ttp)
REVERT: N   29 PHE cc_start: 0.4388 (t80) cc_final: 0.3828 (t80)
REVERT: N   34 MET cc_start: 0.6323 (mmm) cc_final: 0.5917 (mmm)
REVERT: R  154 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5912 (mp0)
REVERT: R  215 GLU cc_start: 0.7265 (tp30) cc_final: 0.6982 (tp30)
REVERT: R  263 ILE cc_start: 0.8078 (pp) cc_final: 0.7860 (tt)
REVERT: R  293 TYR cc_start: 0.7446 (t80) cc_final: 0.7190 (t80)
REVERT: R  328 PHE cc_start: 0.6505 (m-80) cc_final: 0.4622 (t80)
  outliers start: 40
  outliers final: 24
  residues processed: 146
  average time/residue: 0.4100
  time to fit residues: 65.0429
Evaluate side-chains
  131 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain R residue   83 ASN
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  290 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0070
   chunk 6 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
** R 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.222543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.183476 restraints weight = 9065.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 1.78
r_work: 0.3930 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3797 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
moved from start:          0.5664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8278  Z= 0.124
  Angle     :  0.595   9.506  11221  Z= 0.306
  Chirality :  0.042   0.152   1288
  Planarity :  0.004   0.042   1413
  Dihedral  :  4.352  19.033   1204
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 20.45 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.27), residues: 1012
  helix:  2.20 (0.26), residues: 398
  sheet: -0.74 (0.35), residues: 191
  loop : -1.03 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 300 
 TYR   0.024   0.002   TYR R  54 
 PHE   0.015   0.001   PHE B 156 
 TRP   0.025   0.002   TRP R 172 
 HIS   0.006   0.001   HIS R 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8276)
  covalent geometry    : angle       0.59327 (11217)
  SS BOND              : bond        0.00020 (    2)
  SS BOND              : angle       2.36033 (    4)
  hydrogen bonds       : bond        0.03458 (  406)
  hydrogen bonds       : angle       4.37708 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.6907 (p0) cc_final: 0.6701 (p0)
REVERT: A  235 GLU cc_start: 0.6312 (mm-30) cc_final: 0.5987 (tp30)
REVERT: B  274 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6966 (pp)
REVERT: B  330 MET cc_start: 0.5758 (tpp) cc_final: 0.4619 (ttp)
REVERT: N   29 PHE cc_start: 0.4390 (t80) cc_final: 0.3825 (t80)
REVERT: N   34 MET cc_start: 0.6329 (mmm) cc_final: 0.5918 (mmm)
REVERT: R  115 PHE cc_start: 0.5300 (OUTLIER) cc_final: 0.4454 (p90)
REVERT: R  154 GLU cc_start: 0.6478 (mt-10) cc_final: 0.5959 (mp0)
REVERT: R  215 GLU cc_start: 0.7215 (tp30) cc_final: 0.6950 (tp30)
REVERT: R  263 ILE cc_start: 0.8066 (pp) cc_final: 0.7846 (tt)
REVERT: R  293 TYR cc_start: 0.7441 (t80) cc_final: 0.7216 (t80)
REVERT: R  328 PHE cc_start: 0.6578 (m-80) cc_final: 0.4657 (t80)
  outliers start: 33
  outliers final: 19
  residues processed: 134
  average time/residue: 0.4071
  time to fit residues: 59.1666
Evaluate side-chains
  122 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  290 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0770
   chunk 77 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.223061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.184544 restraints weight = 9038.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 1.76
r_work: 0.3948 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3818 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6339
moved from start:          0.5769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8278  Z= 0.114
  Angle     :  0.583   9.204  11221  Z= 0.299
  Chirality :  0.041   0.175   1288
  Planarity :  0.004   0.041   1413
  Dihedral  :  4.227  19.008   1204
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.11 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.27), residues: 1012
  helix:  2.26 (0.26), residues: 398
  sheet: -0.61 (0.36), residues: 186
  loop : -1.01 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  32 
 TYR   0.022   0.001   TYR R  54 
 PHE   0.015   0.001   PHE B 156 
 TRP   0.030   0.002   TRP R 172 
 HIS   0.006   0.001   HIS R 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8276)
  covalent geometry    : angle       0.58203 (11217)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       1.56779 (    4)
  hydrogen bonds       : bond        0.03282 (  406)
  hydrogen bonds       : angle       4.29776 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6007 (tp30)
REVERT: B  274 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (pp)
REVERT: B  330 MET cc_start: 0.5751 (tpp) cc_final: 0.4581 (ttp)
REVERT: N   29 PHE cc_start: 0.4417 (t80) cc_final: 0.3986 (t80)
REVERT: N   34 MET cc_start: 0.6367 (mmm) cc_final: 0.5897 (mmt)
REVERT: N   78 THR cc_start: 0.6030 (OUTLIER) cc_final: 0.5597 (p)
REVERT: R  115 PHE cc_start: 0.4860 (OUTLIER) cc_final: 0.4260 (p90)
REVERT: R  154 GLU cc_start: 0.6529 (mt-10) cc_final: 0.5922 (mp0)
REVERT: R  293 TYR cc_start: 0.7401 (t80) cc_final: 0.7175 (t80)
REVERT: R  328 PHE cc_start: 0.6538 (m-80) cc_final: 0.4666 (t80)
  outliers start: 40
  outliers final: 21
  residues processed: 137
  average time/residue: 0.4011
  time to fit residues: 59.9059
Evaluate side-chains
  123 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  277 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0870
   chunk 98 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 90 optimal weight:    0.3980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6562

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.222846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.184793 restraints weight = 8983.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 1.74
r_work: 0.3954 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6317
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8278  Z= 0.112
  Angle     :  0.597  13.556  11221  Z= 0.301
  Chirality :  0.041   0.181   1288
  Planarity :  0.004   0.041   1413
  Dihedral  :  4.148  18.994   1204
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.58 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.27), residues: 1012
  helix:  2.28 (0.26), residues: 398
  sheet: -0.58 (0.36), residues: 186
  loop : -0.95 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 300 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.017   0.001   PHE A 199 
 TRP   0.039   0.002   TRP R 172 
 HIS   0.006   0.001   HIS R 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8276)
  covalent geometry    : angle       0.59631 (11217)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       1.48386 (    4)
  hydrogen bonds       : bond        0.03253 (  406)
  hydrogen bonds       : angle       4.28128 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.6826 (p0) cc_final: 0.6607 (p0)
REVERT: B  274 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6999 (pp)
REVERT: B  297 PHE cc_start: 0.6818 (m-10) cc_final: 0.5895 (m-10)
REVERT: B  330 MET cc_start: 0.5597 (tpp) cc_final: 0.4486 (ttp)
REVERT: N   29 PHE cc_start: 0.4350 (t80) cc_final: 0.3898 (t80)
REVERT: N   34 MET cc_start: 0.6369 (mmm) cc_final: 0.5933 (mmm)
REVERT: N   78 THR cc_start: 0.6017 (OUTLIER) cc_final: 0.5599 (p)
REVERT: R  115 PHE cc_start: 0.5262 (OUTLIER) cc_final: 0.4513 (p90)
REVERT: R  154 GLU cc_start: 0.6538 (mt-10) cc_final: 0.5918 (mp0)
REVERT: R  268 ARG cc_start: 0.7722 (tmt170) cc_final: 0.7511 (tmt170)
REVERT: R  293 TYR cc_start: 0.7368 (t80) cc_final: 0.7102 (t80)
REVERT: R  328 PHE cc_start: 0.6486 (m-80) cc_final: 0.4640 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 130
  average time/residue: 0.4151
  time to fit residues: 58.7556
Evaluate side-chains
  122 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  277 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.223118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.184126 restraints weight = 9033.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 1.80
r_work: 0.3947 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3815 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.6009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8278  Z= 0.126
  Angle     :  0.619  12.102  11221  Z= 0.315
  Chirality :  0.042   0.189   1288
  Planarity :  0.004   0.050   1413
  Dihedral  :  4.274  19.274   1204
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.15 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.27), residues: 1012
  helix:  2.27 (0.26), residues: 395
  sheet: -0.73 (0.35), residues: 191
  loop : -0.96 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 284 
 TYR   0.021   0.001   TYR R  54 
 PHE   0.014   0.002   PHE B 297 
 TRP   0.037   0.002   TRP R 172 
 HIS   0.005   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8276)
  covalent geometry    : angle       0.61845 (11217)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       1.57240 (    4)
  hydrogen bonds       : bond        0.03424 (  406)
  hydrogen bonds       : angle       4.34811 ( 1164)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  274 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7039 (pp)
REVERT: B  330 MET cc_start: 0.5669 (tpp) cc_final: 0.4567 (ttp)
REVERT: N   29 PHE cc_start: 0.4352 (t80) cc_final: 0.3947 (t80)
REVERT: N   34 MET cc_start: 0.6310 (mmm) cc_final: 0.5881 (mmm)
REVERT: N   78 THR cc_start: 0.6020 (OUTLIER) cc_final: 0.5563 (p)
REVERT: N   80 TYR cc_start: 0.6558 (m-80) cc_final: 0.6346 (m-80)
REVERT: R  115 PHE cc_start: 0.5290 (OUTLIER) cc_final: 0.4522 (p90)
REVERT: R  154 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5948 (mp0)
REVERT: R  328 PHE cc_start: 0.6570 (m-80) cc_final: 0.4664 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 130
  average time/residue: 0.4310
  time to fit residues: 60.6720
Evaluate side-chains
  121 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  142 SER
Chi-restraints excluded: chain R residue  277 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    8.9990
   chunk 56 optimal weight:    8.9990
   chunk 32 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
N  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.223333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.185010 restraints weight = 9076.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 1.76
r_work: 0.3959 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3826 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6334
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8278  Z= 0.120
  Angle     :  0.626  11.915  11221  Z= 0.318
  Chirality :  0.042   0.204   1288
  Planarity :  0.005   0.058   1413
  Dihedral  :  4.296  25.198   1204
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 22.82 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.27), residues: 1012
  helix:  2.25 (0.26), residues: 395
  sheet: -0.72 (0.35), residues: 191
  loop : -0.92 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A  32 
 TYR   0.020   0.001   TYR R  54 
 PHE   0.029   0.001   PHE A 343 
 TRP   0.042   0.002   TRP R 172 
 HIS   0.005   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8276)
  covalent geometry    : angle       0.62156 (11217)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       3.88275 (    4)
  hydrogen bonds       : bond        0.03320 (  406)
  hydrogen bonds       : angle       4.34687 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3400.74 seconds
wall clock time: 58 minutes 39.37 seconds (3519.37 seconds total)