Starting phenix.real_space_refine
on Fri Aug 22 21:19:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uxv_42786/08_2025/8uxv_42786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uxv_42786/08_2025/8uxv_42786.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uxv_42786/08_2025/8uxv_42786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uxv_42786/08_2025/8uxv_42786.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uxv_42786/08_2025/8uxv_42786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uxv_42786/08_2025/8uxv_42786.map"
  }
  resolution = 3.2
  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=   0.001 sd=   0.098
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5149      2.51       5
     N    1407      2.21       5
     O    1453      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8065
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "X"
      Number of atoms: 1696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1696
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 5, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 182
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 10, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 102
    Chain: "Y"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "Z"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 2378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2378
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 15, 'TRANS': 284}
  Time building chain proxies: 1.52, per 1000 atoms: 0.19
  Number of scatterers: 8065
  At special positions: 0
  Unit cell: (119.601, 103.887, 99.522, 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      56     16.00
     O    1453      8.00
     N    1407      7.00
     C    5149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 170 " - pdb=" SG  CYS A 190 " distance=2.04

  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: 0.56
  Conformation dependent library (CDL) restraints added in 342.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      43.6% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.610A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.647A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.912A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 15 through 40
      removed outlier: 3.889A  pdb=" N   THR X  40 " --> pdb=" O   VAL X  36 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 52 through 60
      removed outlier: 3.618A  pdb=" N   MET X  60 " --> pdb=" O   ILE X  56 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 233 through 239
      removed outlier: 3.805A  pdb=" N   GLN X 236 " --> pdb=" O   LYS X 233 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASN X 239 " --> pdb=" O   GLN X 236 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 265 through 278
      removed outlier: 3.619A  pdb=" N   ALA X 269 " --> pdb=" O   ARG X 265 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 293 through 304
      removed outlier: 3.594A  pdb=" N   LEU X 297 " --> pdb=" O   LYS X 293 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 312 through 318
      removed outlier: 3.512A  pdb=" N   ALA X 316 " --> pdb=" O   PRO X 313 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TYR X 318 " --> pdb=" O   PHE X 315 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 331 through 352
      removed outlier: 3.894A  pdb=" N   THR X 335 " --> pdb=" O   ASP X 331 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   SER X 352 " --> pdb=" O   ILE X 348 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 370 through 391
    Processing helix  chain 'Y' and resid 4 through 25
    Processing helix  chain 'Y' and resid 29 through 34
    Processing helix  chain 'Y' and resid 35 through 37
      No H-bonds generated for 'chain 'Y' and resid 35 through 37'
    Processing helix  chain 'Z' and resid 8 through 24
      removed outlier: 3.839A  pdb=" N   ASN Z  24 " --> pdb=" O   LYS Z  20 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 29 through 45
      removed outlier: 3.661A  pdb=" N   ALA Z  33 " --> pdb=" O   LYS Z  29 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 46 through 48
      No H-bonds generated for 'chain 'Z' and resid 46 through 48'
    Processing helix  chain 'A' and resid 20 through 24
      removed outlier: 3.937A  pdb=" N   ALA A  23 " --> pdb=" O   GLY A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 53
      removed outlier: 3.626A  pdb=" N   PHE A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 57
      removed outlier: 3.609A  pdb=" N   HIS A  57 " --> pdb=" O   PRO A  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 54 through 57'
    Processing helix  chain 'A' and resid 58 through 88
      removed outlier: 3.699A  pdb=" N   PHE A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
      Proline residue:  A  80  - end of helix
    Processing helix  chain 'A' and resid 94 through 129
      removed outlier: 3.628A  pdb=" N   CYS A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS A 106 " --> pdb=" O   MET A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 157
      removed outlier: 3.598A  pdb=" N   LEU A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ILE A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
      removed outlier: 3.614A  pdb=" N   PHE A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LEU A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 186
    Processing helix  chain 'A' and resid 187 through 189
      No H-bonds generated for 'chain 'A' and resid 187 through 189'
    Processing helix  chain 'A' and resid 193 through 228
      removed outlier: 3.759A  pdb=" N   MET A 208 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LEU A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   ASP A 211 " --> pdb=" O   THR A 207 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   SER A 212 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   GLY A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 266
      removed outlier: 3.743A  pdb=" N   LYS A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   PHE A 252 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      Proline residue:  A 255  - end of helix
      removed outlier: 3.572A  pdb=" N   LEU A 259 " --> pdb=" O   PRO A 255 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER A 260 " --> pdb=" O   MET A 256 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ARG A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 284
      removed outlier: 4.088A  pdb=" N   HIS A 274 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 294
      Proline residue:  A 290  - end of helix
    Processing helix  chain 'A' and resid 297 through 310
      removed outlier: 3.941A  pdb=" N   ARG A 303 " --> pdb=" O   GLN A 299 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.581A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.162A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'X' and resid 210 through 214
      removed outlier: 7.219A  pdb=" N   ARG X  42 " --> pdb=" O   ALA X 243 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ILE X 245 " --> pdb=" O   ARG X  42 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   LEU X  44 " --> pdb=" O   ILE X 245 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   VAL X 247 " --> pdb=" O   LEU X  44 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   LEU X  46 " --> pdb=" O   VAL X 247 " (cutoff:3.500A)
      removed outlier: 8.882A  pdb=" N   ASP X 249 " --> pdb=" O   LEU X  46 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ILE X 244 " --> pdb=" O   ILE X 288 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   PHE X 290 " --> pdb=" O   ILE X 244 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   PHE X 246 " --> pdb=" O   PHE X 290 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ASN X 292 " --> pdb=" O   PHE X 246 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL X 248 " --> pdb=" O   ASN X 292 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 46 through 51
      removed outlier: 6.572A  pdb=" N   ILE Y 338 " --> pdb=" O   ARG Y  48 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR Y  50 " --> pdb=" O   LEU Y 336 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU Y 336 " --> pdb=" O   THR Y  50 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   CYS Y 317 " --> pdb=" O   GLY Y 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 58 through 63
      removed outlier: 4.100A  pdb=" N   ALA Y  60 " --> pdb=" O   ALA Y  73 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS Y  78 " --> pdb=" O   SER Y  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 100 through 105
      removed outlier: 6.894A  pdb=" N   GLY Y 115 " --> pdb=" O   MET Y 101 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   CYS Y 103 " --> pdb=" O   ALA Y 113 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ALA Y 113 " --> pdb=" O   CYS Y 103 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   TYR Y 105 " --> pdb=" O   TYR Y 111 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   TYR Y 111 " --> pdb=" O   TYR Y 105 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   GLY Y 116 " --> pdb=" O   ILE Y 120 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   ILE Y 120 " --> pdb=" O   GLY Y 116 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   CYS Y 121 " --> pdb=" O   GLU Y 138 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLU Y 138 " --> pdb=" O   CYS Y 121 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE Y 123 " --> pdb=" O   SER Y 136 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG Y 134 " --> pdb=" O   ASN Y 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 146 through 151
      removed outlier: 3.562A  pdb=" N   ILE Y 157 " --> pdb=" O   TRP Y 169 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR Y 165 " --> pdb=" O   SER Y 161 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ASP Y 170 " --> pdb=" O   GLN Y 176 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   GLN Y 176 " --> pdb=" O   ASP Y 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'Y' and resid 187 through 192
      removed outlier: 6.734A  pdb=" N   GLY Y 202 " --> pdb=" O   MET Y 188 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LEU Y 190 " --> pdb=" O   VAL Y 200 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL Y 200 " --> pdb=" O   LEU Y 190 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   LEU Y 192 " --> pdb=" O   LEU Y 198 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   LEU Y 198 " --> pdb=" O   LEU Y 192 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA Y 208 " --> pdb=" O   THR Y 221 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   THR Y 221 " --> pdb=" O   ALA Y 208 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU Y 210 " --> pdb=" O   ARG Y 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'Y' and resid 229 through 234
      removed outlier: 6.608A  pdb=" N   GLY Y 244 " --> pdb=" O   ASN Y 230 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE Y 232 " --> pdb=" O   ALA Y 242 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ALA Y 242 " --> pdb=" O   ILE Y 232 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   PHE Y 234 " --> pdb=" O   ALA Y 240 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ALA Y 240 " --> pdb=" O   PHE Y 234 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS Y 250 " --> pdb=" O   THR Y 263 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   THR Y 263 " --> pdb=" O   CYS Y 250 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU Y 252 " --> pdb=" O   LEU Y 261 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN Y 259 " --> pdb=" O   ASP Y 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'Y' and resid 273 through 278
      removed outlier: 3.915A  pdb=" N   SER Y 275 " --> pdb=" O   GLY Y 288 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   CYS Y 294 " --> pdb=" O   VAL Y 307 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   VAL Y 307 " --> pdb=" O   CYS Y 294 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL Y 296 " --> pdb=" O   ALA Y 305 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 13 through 14

    398 hydrogen bonds defined for protein.
    1137 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: 0.88

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2623
        1.34 -     1.46: 1951
        1.46 -     1.58: 3580
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 8235
  Sorted by residual:
  bond pdb=" N   GLY X 304 "
       pdb=" CA  GLY X 304 "
    ideal  model  delta    sigma   weight residual
    1.454  1.496 -0.041 1.45e-02 4.76e+03 8.10e+00
  bond pdb=" C   VAL A 254 "
       pdb=" N   PRO A 255 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 8.40e-03 1.42e+04 6.85e+00
  bond pdb=" CA  GLY X 304 "
       pdb=" C   GLY X 304 "
    ideal  model  delta    sigma   weight residual
    1.513  1.532 -0.019 1.06e-02 8.90e+03 3.19e+00
  bond pdb=" C   ALA X 303 "
       pdb=" N   GLY X 304 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.00e-02 1.00e+04 2.85e+00
  bond pdb=" N   GLY X 353 "
       pdb=" CA  GLY X 353 "
    ideal  model  delta    sigma   weight residual
    1.449  1.473 -0.024 1.45e-02 4.76e+03 2.77e+00
  ... (remaining 8230 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 10970
        1.61 -     3.22: 165
        3.22 -     4.83: 27
        4.83 -     6.44: 6
        6.44 -     8.04: 3
  Bond angle restraints: 11171
  Sorted by residual:
  angle pdb=" C   VAL A 280 "
        pdb=" N   TYR A 281 "
        pdb=" CA  TYR A 281 "
      ideal   model   delta    sigma   weight residual
     121.18  114.12    7.06 1.98e+00 2.55e-01 1.27e+01
  angle pdb=" CA  MET A 208 "
        pdb=" CB  MET A 208 "
        pdb=" CG  MET A 208 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.31e+00
  angle pdb=" CB  MET A 208 "
        pdb=" CG  MET A 208 "
        pdb=" SD  MET A 208 "
      ideal   model   delta    sigma   weight residual
     112.70  104.66    8.04 3.00e+00 1.11e-01 7.19e+00
  angle pdb=" N   TYR A 281 "
        pdb=" CA  TYR A 281 "
        pdb=" CB  TYR A 281 "
      ideal   model   delta    sigma   weight residual
     110.39  114.66   -4.27 1.75e+00 3.27e-01 5.95e+00
  angle pdb=" N   MET A 208 "
        pdb=" CA  MET A 208 "
        pdb=" CB  MET A 208 "
      ideal   model   delta    sigma   weight residual
     111.01  107.29    3.72 1.56e+00 4.11e-01 5.70e+00
  ... (remaining 11166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4398
       17.73 -    35.46: 402
       35.46 -    53.19: 76
       53.19 -    70.92: 14
       70.92 -    88.65: 6
  Dihedral angle restraints: 4896
    sinusoidal: 1869
      harmonic: 3027
  Sorted by residual:
  dihedral pdb=" CB  CYS A 170 "
           pdb=" SG  CYS A 170 "
           pdb=" SG  CYS A 190 "
           pdb=" CB  CYS A 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.85   40.85     1      1.00e+01 1.00e-02 2.34e+01
  dihedral pdb=" CB  CYS A  98 "
           pdb=" SG  CYS A  98 "
           pdb=" SG  CYS A 180 "
           pdb=" CB  CYS A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.25   37.25     1      1.00e+01 1.00e-02 1.96e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.35   20.65     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 4893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 711
       0.027 -    0.054: 340
       0.054 -    0.080: 136
       0.080 -    0.107: 66
       0.107 -    0.134: 31
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  ILE Y 338 "
            pdb=" N   ILE Y 338 "
            pdb=" C   ILE Y 338 "
            pdb=" CB  ILE Y 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE Y  58 "
            pdb=" N   ILE Y  58 "
            pdb=" C   ILE Y  58 "
            pdb=" CB  ILE Y  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE Y 232 "
            pdb=" N   ILE Y 232 "
            pdb=" C   ILE Y 232 "
            pdb=" CB  ILE Y 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1281 not shown)

  Planarity restraints: 1417
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER X 352 "    0.021 2.00e-02 2.50e+03   4.13e-02 1.71e+01
        pdb=" C   SER X 352 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   SER X 352 "    0.027 2.00e-02 2.50e+03
        pdb=" N   GLY X 353 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA X 303 "    0.016 2.00e-02 2.50e+03   3.05e-02 9.33e+00
        pdb=" C   ALA X 303 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ALA X 303 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLY X 304 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 289 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO A 290 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1414 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 82
        2.65 -     3.22: 7069
        3.22 -     3.78: 11556
        3.78 -     4.34: 16030
        4.34 -     4.90: 28148
  Nonbonded interactions: 62885
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 211 "
            pdb=" OH  TYR A 253 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OH  TYR X 391 "
            pdb=" OD2 ASP A 122 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR Y 128 "
            pdb=" O   ASN Y 132 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" NE2 HIS Y  54 "
            pdb=" OG  SER Y  72 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   LEU A 164 "
            pdb=" OH  TYR A 169 "
     model   vdw
     2.287 3.040
  ... (remaining 62880 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:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.750
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
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   0.041   8237  Z= 0.147
  Angle     :  0.526   8.044  11175  Z= 0.281
  Chirality :  0.042   0.134   1284
  Planarity :  0.004   0.051   1417
  Dihedral  : 14.017  88.646   2932
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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 aren not related in a simple way.
  whole:  0.80 (0.27), residues: 1027
  helix:  2.12 (0.28), residues: 382
  sheet:  0.09 (0.34), residues: 229
  loop : -0.70 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Y 197 
 TYR   0.029   0.002   TYR Y  59 
 PHE   0.014   0.001   PHE N 108 
 TRP   0.011   0.001   TRP N  47 
 HIS   0.010   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8235)
  covalent geometry    : angle       0.52584 (11171)
  SS BOND              : bond        0.00399 (    2)
  SS BOND              : angle       0.78886 (    4)
  hydrogen bonds       : bond        0.16551 (  398)
  hydrogen bonds       : angle       5.99238 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.196 
Fit side-chains
REVERT: Y  258 ASP cc_start: 0.6810 (t70) cc_final: 0.6223 (t0)
REVERT: Z   51 LEU cc_start: 0.8869 (tp) cc_final: 0.8652 (tp)
REVERT: A  224 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7725 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0955
  time to fit residues: 14.6468
Evaluate side-chains
  105 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
X  59 GLN
Y 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.171321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.135836 restraints weight = 9441.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.80
r_work: 0.3297 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.0818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8237  Z= 0.120
  Angle     :  0.513   8.954  11175  Z= 0.270
  Chirality :  0.042   0.142   1284
  Planarity :  0.004   0.042   1417
  Dihedral  :  3.891  18.374   1134
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  6.09 %
    Favored  : 92.97 %
  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 aren not related in a simple way.
  whole:  1.00 (0.26), residues: 1027
  helix:  2.36 (0.28), residues: 383
  sheet:  0.41 (0.36), residues: 222
  loop : -0.80 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Y 197 
 TYR   0.012   0.001   TYR A 281 
 PHE   0.013   0.001   PHE N 108 
 TRP   0.011   0.001   TRP N  47 
 HIS   0.008   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8235)
  covalent geometry    : angle       0.51265 (11171)
  SS BOND              : bond        0.00424 (    2)
  SS BOND              : angle       1.06767 (    4)
  hydrogen bonds       : bond        0.04763 (  398)
  hydrogen bonds       : angle       4.46303 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.270 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8197 (ttt-90)
REVERT: Y  175 GLN cc_start: 0.8194 (mp10) cc_final: 0.7746 (mp10)
REVERT: Z   51 LEU cc_start: 0.8719 (tp) cc_final: 0.8473 (tp)
REVERT: A  224 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7484 (tttm)
  outliers start: 8
  outliers final: 4
  residues processed: 115
  average time/residue: 0.0804
  time to fit residues: 12.7302
Evaluate side-chains
  110 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain A residue  251 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
X  23 ASN
Y  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.168424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.131787 restraints weight = 9384.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.89
r_work: 0.3198 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8237  Z= 0.152
  Angle     :  0.534   9.462  11175  Z= 0.279
  Chirality :  0.042   0.139   1284
  Planarity :  0.004   0.041   1417
  Dihedral  :  3.980  16.528   1134
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.67 %
    Favored  : 89.70 %
  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 aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1027
  helix:  2.39 (0.27), residues: 379
  sheet:  0.34 (0.35), residues: 217
  loop : -0.79 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Y 197 
 TYR   0.014   0.002   TYR X 339 
 PHE   0.018   0.001   PHE N 108 
 TRP   0.014   0.002   TRP N  47 
 HIS   0.011   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8235)
  covalent geometry    : angle       0.53368 (11171)
  SS BOND              : bond        0.00488 (    2)
  SS BOND              : angle       1.03364 (    4)
  hydrogen bonds       : bond        0.05261 (  398)
  hydrogen bonds       : angle       4.33469 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.207 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8257 (ttt-90)
REVERT: X  223 ASP cc_start: 0.9009 (t0) cc_final: 0.8797 (t0)
REVERT: Y   78 LYS cc_start: 0.9260 (tppt) cc_final: 0.8999 (tppt)
REVERT: Y  175 GLN cc_start: 0.8193 (mp10) cc_final: 0.7681 (mp10)
REVERT: Z   42 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7505 (mp0)
REVERT: A  224 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7520 (tttm)
  outliers start: 14
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0799
  time to fit residues: 11.7934
Evaluate side-chains
  107 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   65 THR
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0770
   chunk 80 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.171573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.138095 restraints weight = 9564.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.13
r_work: 0.3231 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8237  Z= 0.101
  Angle     :  0.465   8.579  11175  Z= 0.245
  Chirality :  0.040   0.133   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.746  15.756   1134
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.19 %
    Favored  : 88.41 %
  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 aren not related in a simple way.
  whole:  1.08 (0.27), residues: 1027
  helix:  2.46 (0.27), residues: 386
  sheet:  0.25 (0.35), residues: 220
  loop : -0.68 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG Y 197 
 TYR   0.015   0.001   TYR A 219 
 PHE   0.012   0.001   PHE N 108 
 TRP   0.012   0.001   TRP X 234 
 HIS   0.006   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 8235)
  covalent geometry    : angle       0.46440 (11171)
  SS BOND              : bond        0.00436 (    2)
  SS BOND              : angle       0.97061 (    4)
  hydrogen bonds       : bond        0.04182 (  398)
  hydrogen bonds       : angle       4.11092 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.290 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8308 (ttt-90)
REVERT: Y   78 LYS cc_start: 0.9247 (tppt) cc_final: 0.9020 (tppt)
REVERT: Y  175 GLN cc_start: 0.8156 (mp10) cc_final: 0.7694 (mp10)
REVERT: Z   42 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7523 (mp0)
REVERT: A  224 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7651 (tttm)
  outliers start: 12
  outliers final: 9
  residues processed: 99
  average time/residue: 0.0847
  time to fit residues: 11.4278
Evaluate side-chains
  96 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain Y residue   29 THR
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  288 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.162056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.125672 restraints weight = 9494.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.85
r_work: 0.3150 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   8237  Z= 0.333
  Angle     :  0.706   9.496  11175  Z= 0.367
  Chirality :  0.049   0.150   1284
  Planarity :  0.005   0.043   1417
  Dihedral  :  4.607  16.342   1134
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.23 %
    Favored  : 84.78 %
  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 aren not related in a simple way.
  whole:  0.44 (0.26), residues: 1027
  helix:  1.80 (0.27), residues: 383
  sheet:  0.26 (0.35), residues: 218
  loop : -1.10 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 141 
 TYR   0.021   0.003   TYR X 339 
 PHE   0.031   0.003   PHE N 108 
 TRP   0.023   0.003   TRP N  47 
 HIS   0.017   0.002   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00847 ( 8235)
  covalent geometry    : angle       0.70626 (11171)
  SS BOND              : bond        0.00612 (    2)
  SS BOND              : angle       1.20236 (    4)
  hydrogen bonds       : bond        0.07741 (  398)
  hydrogen bonds       : angle       4.68541 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.327 
Fit side-chains
REVERT: Y   96 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7692 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8319 (mp10) cc_final: 0.7729 (mp10)
REVERT: Z   42 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7262 (mt-10)
REVERT: A  162 PHE cc_start: 0.6836 (t80) cc_final: 0.6595 (t80)
REVERT: A  211 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7321 (t70)
REVERT: A  224 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7652 (tttm)
  outliers start: 17
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1030
  time to fit residues: 15.6983
Evaluate side-chains
  112 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain X residue  213 GLN
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   96 ARG
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  213 VAL
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  270 ILE
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  288 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.165832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.129516 restraints weight = 9440.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.85
r_work: 0.3105 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8237  Z= 0.170
  Angle     :  0.547   8.534  11175  Z= 0.287
  Chirality :  0.043   0.138   1284
  Planarity :  0.004   0.042   1417
  Dihedral  :  4.243  15.919   1134
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.69 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1027
  helix:  2.03 (0.27), residues: 385
  sheet:  0.30 (0.35), residues: 218
  loop : -1.10 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 141 
 TYR   0.015   0.002   TYR A 219 
 PHE   0.018   0.001   PHE N 108 
 TRP   0.018   0.002   TRP N  47 
 HIS   0.010   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8235)
  covalent geometry    : angle       0.54690 (11171)
  SS BOND              : bond        0.00540 (    2)
  SS BOND              : angle       1.03492 (    4)
  hydrogen bonds       : bond        0.05636 (  398)
  hydrogen bonds       : angle       4.40433 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.372 
Fit side-chains
REVERT: X  378 ASP cc_start: 0.8299 (m-30) cc_final: 0.8048 (m-30)
REVERT: Y   96 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7645 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8243 (mp10) cc_final: 0.7671 (mp10)
REVERT: Y  186 ASP cc_start: 0.8538 (m-30) cc_final: 0.8229 (m-30)
REVERT: Z   42 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7364 (mp0)
REVERT: A   53 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7346 (mt-10)
REVERT: A  162 PHE cc_start: 0.6805 (t80) cc_final: 0.6566 (t80)
REVERT: A  211 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.7063 (t70)
REVERT: A  224 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7602 (tttm)
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1121
  time to fit residues: 15.6349
Evaluate side-chains
  104 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain X residue  224 VAL
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   96 ARG
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0270
   chunk 100 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7844

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.168671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.132682 restraints weight = 9506.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.85
r_work: 0.3242 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8237  Z= 0.117
  Angle     :  0.493   8.499  11175  Z= 0.259
  Chirality :  0.041   0.135   1284
  Planarity :  0.004   0.040   1417
  Dihedral  :  3.960  15.924   1134
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.46 %
    Favored  : 82.67 %
  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 aren not related in a simple way.
  whole:  0.85 (0.27), residues: 1027
  helix:  2.33 (0.27), residues: 385
  sheet:  0.26 (0.35), residues: 217
  loop : -0.95 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Y 197 
 TYR   0.012   0.001   TYR A 219 
 PHE   0.013   0.001   PHE Y 241 
 TRP   0.014   0.001   TRP X 234 
 HIS   0.006   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8235)
  covalent geometry    : angle       0.49256 (11171)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       0.99061 (    4)
  hydrogen bonds       : bond        0.04570 (  398)
  hydrogen bonds       : angle       4.17879 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.326 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8267 (ttt-90)
REVERT: X  378 ASP cc_start: 0.8266 (m-30) cc_final: 0.8044 (m-30)
REVERT: Y   96 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7582 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8236 (mp10) cc_final: 0.7666 (mp10)
REVERT: Z   42 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7513 (mp0)
REVERT: A  224 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7468 (tttm)
  outliers start: 16
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0986
  time to fit residues: 13.1795
Evaluate side-chains
  101 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain X residue  224 VAL
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   96 ARG
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  270 ILE
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.165037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.128816 restraints weight = 9470.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.85
r_work: 0.3124 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8237  Z= 0.203
  Angle     :  0.585  11.065  11175  Z= 0.303
  Chirality :  0.044   0.141   1284
  Planarity :  0.004   0.042   1417
  Dihedral  :  4.224  16.934   1134
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.39 %
    Favored  : 81.73 %
  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 aren not related in a simple way.
  whole:  0.70 (0.26), residues: 1027
  helix:  2.11 (0.27), residues: 385
  sheet:  0.36 (0.35), residues: 218
  loop : -1.06 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 197 
 TYR   0.016   0.002   TYR A 253 
 PHE   0.020   0.002   PHE N 108 
 TRP   0.018   0.002   TRP N  47 
 HIS   0.011   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 8235)
  covalent geometry    : angle       0.58471 (11171)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       1.06395 (    4)
  hydrogen bonds       : bond        0.05893 (  398)
  hydrogen bonds       : angle       4.37858 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.217 
Fit side-chains
REVERT: X  378 ASP cc_start: 0.8317 (m-30) cc_final: 0.8051 (m-30)
REVERT: Y   96 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7620 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8270 (mp10) cc_final: 0.7712 (mp10)
REVERT: Y  186 ASP cc_start: 0.8526 (m-30) cc_final: 0.8204 (m-30)
REVERT: Z   42 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7388 (mp0)
REVERT: A  162 PHE cc_start: 0.6783 (t80) cc_final: 0.6551 (t80)
REVERT: A  224 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7552 (tttm)
  outliers start: 16
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1058
  time to fit residues: 14.4578
Evaluate side-chains
  107 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain X residue  214 VAL
Chi-restraints excluded: chain X residue  224 VAL
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   65 THR
Chi-restraints excluded: chain Y residue   96 ARG
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  213 VAL
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  270 ILE
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.168060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.134236 restraints weight = 9458.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.13
r_work: 0.3208 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8237  Z= 0.127
  Angle     :  0.510   9.202  11175  Z= 0.266
  Chirality :  0.042   0.136   1284
  Planarity :  0.004   0.040   1417
  Dihedral  :  4.017  17.498   1134
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.39 %
    Favored  : 81.73 %
  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 aren not related in a simple way.
  whole:  0.88 (0.27), residues: 1027
  helix:  2.30 (0.27), residues: 382
  sheet:  0.43 (0.36), residues: 212
  loop : -0.93 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 197 
 TYR   0.013   0.001   TYR A 219 
 PHE   0.013   0.001   PHE N 108 
 TRP   0.015   0.002   TRP N  47 
 HIS   0.007   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8235)
  covalent geometry    : angle       0.50974 (11171)
  SS BOND              : bond        0.00476 (    2)
  SS BOND              : angle       0.98995 (    4)
  hydrogen bonds       : bond        0.04766 (  398)
  hydrogen bonds       : angle       4.20793 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.316 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8286 (ttt-90)
REVERT: X  378 ASP cc_start: 0.8208 (m-30) cc_final: 0.7995 (m-30)
REVERT: Y   96 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7637 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8259 (mp10) cc_final: 0.7772 (mp10)
REVERT: Z   42 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7591 (mp0)
REVERT: A  224 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7617 (tttm)
  outliers start: 16
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1108
  time to fit residues: 14.6065
Evaluate side-chains
  104 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain X residue  214 VAL
Chi-restraints excluded: chain X residue  224 VAL
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   65 THR
Chi-restraints excluded: chain Y residue   96 ARG
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  213 VAL
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  270 ILE
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.168728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.134526 restraints weight = 9488.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.25
r_work: 0.3210 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8237  Z= 0.125
  Angle     :  0.503   7.696  11175  Z= 0.263
  Chirality :  0.042   0.134   1284
  Planarity :  0.004   0.040   1417
  Dihedral  :  3.941  19.761   1134
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.51 %
    Favored  : 81.50 %
  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 aren not related in a simple way.
  whole:  0.95 (0.27), residues: 1027
  helix:  2.38 (0.27), residues: 382
  sheet:  0.32 (0.35), residues: 218
  loop : -0.83 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 197 
 TYR   0.013   0.001   TYR A 219 
 PHE   0.013   0.001   PHE N 108 
 TRP   0.014   0.001   TRP N  47 
 HIS   0.006   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8235)
  covalent geometry    : angle       0.50256 (11171)
  SS BOND              : bond        0.00433 (    2)
  SS BOND              : angle       0.99449 (    4)
  hydrogen bonds       : bond        0.04630 (  398)
  hydrogen bonds       : angle       4.15199 ( 1137)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.319 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8306 (ttt-90)
REVERT: Y   96 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7626 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8254 (mp10) cc_final: 0.7749 (mp10)
REVERT: Z   42 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7581 (mp0)
REVERT: A  224 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7551 (tttm)
  outliers start: 17
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0994
  time to fit residues: 13.0202
Evaluate side-chains
  103 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain X residue  214 VAL
Chi-restraints excluded: chain X residue  224 VAL
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue   65 THR
Chi-restraints excluded: chain Y residue   96 ARG
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  213 VAL
Chi-restraints excluded: chain Y residue  234 PHE
Chi-restraints excluded: chain Y residue  270 ILE
Chi-restraints excluded: chain Y residue  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 27 optimal weight:    0.0050
   chunk 51 optimal weight:    0.3980
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.171035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.137632 restraints weight = 9441.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.04
r_work: 0.3275 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8237  Z= 0.100
  Angle     :  0.469   7.159  11175  Z= 0.247
  Chirality :  0.041   0.132   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.753  17.647   1134
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.56 %
    Favored  : 81.38 %
  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 aren not related in a simple way.
  whole:  1.07 (0.27), residues: 1027
  helix:  2.50 (0.28), residues: 386
  sheet:  0.33 (0.35), residues: 220
  loop : -0.79 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Y 197 
 TYR   0.011   0.001   TYR A 219 
 PHE   0.012   0.001   PHE Y 241 
 TRP   0.015   0.001   TRP X 234 
 HIS   0.004   0.001   HIS X 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8235)
  covalent geometry    : angle       0.46892 (11171)
  SS BOND              : bond        0.00380 (    2)
  SS BOND              : angle       0.93867 (    4)
  hydrogen bonds       : bond        0.03949 (  398)
  hydrogen bonds       : angle       4.02646 ( 1137)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2220.91 seconds
wall clock time: 38 minutes 37.80 seconds (2317.80 seconds total)