Starting phenix.real_space_refine
on Wed Jan 15 05:16:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uxv_42786/01_2025/8uxv_42786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uxv_42786/01_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uxv_42786/01_2025/8uxv_42786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uxv_42786/01_2025/8uxv_42786.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uxv_42786/01_2025/8uxv_42786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uxv_42786/01_2025/8uxv_42786.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 10}
          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: 5.11, per 1000 atoms: 0.63
  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: 1.88
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.82
  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: 2.17

  Time building geometry restraints manager: 2.21 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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.640
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.250
-------------------------------------------------------------------------------
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   8235  Z= 0.208
  Angle     :  0.526   8.044  11171  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.011   0.001   TRP N  47 
 HIS   0.010   0.001   HIS X 357 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.029   0.002   TYR Y  59 
 ARG   0.005   0.000   ARG Y 197 

*********************** 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  : 0.939 
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: 0.2272
  time to fit residues: 34.7705
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  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.169002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.133793 restraints weight = 9302.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.24
r_work: 0.3142 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.0811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8235  Z= 0.246
  Angle     :  0.547   8.552  11171  Z= 0.287
  Chirality :  0.043   0.145   1284
  Planarity :  0.004   0.043   1417
  Dihedral  :  4.043  19.623   1134
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  6.56 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1027
  helix:  2.31 (0.27), residues: 379
  sheet:  0.37 (0.36), residues: 222
  loop : -0.84 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP N  47 
 HIS   0.011   0.001   HIS X 357 
 PHE   0.016   0.001   PHE N 108 
 TYR   0.014   0.002   TYR A 281 
 ARG   0.003   0.000   ARG Y 197 

*********************** 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
  119 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.909 
Fit side-chains
REVERT: Y  175 GLN cc_start: 0.8214 (mp10) cc_final: 0.7808 (mp10)
REVERT: Z   51 LEU cc_start: 0.8824 (tp) cc_final: 0.8561 (tp)
REVERT: A  224 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7626 (tttm)
  outliers start: 10
  outliers final: 5
  residues processed: 112
  average time/residue: 0.2030
  time to fit residues: 31.1303
Evaluate side-chains
  107 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
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   65 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 90 optimal weight:    0.0060
   chunk 1 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
X  23 ASN
** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  88 ASN
A 173 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.168572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.134848 restraints weight = 9451.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.10
r_work: 0.3190 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8235  Z= 0.238
  Angle     :  0.527   9.162  11171  Z= 0.276
  Chirality :  0.042   0.137   1284
  Planarity :  0.004   0.041   1417
  Dihedral  :  4.002  16.220   1134
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  8.90 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1027
  helix:  2.35 (0.27), residues: 379
  sheet:  0.31 (0.35), residues: 217
  loop : -0.82 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N  47 
 HIS   0.010   0.001   HIS X 357 
 PHE   0.016   0.001   PHE N 108 
 TYR   0.013   0.001   TYR X 339 
 ARG   0.003   0.000   ARG Y 197 

*********************** 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
  117 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.915 
Fit side-chains
REVERT: Y   78 LYS cc_start: 0.9247 (tppt) cc_final: 0.9001 (tppt)
REVERT: Y  175 GLN cc_start: 0.8195 (mp10) cc_final: 0.7760 (mp10)
REVERT: Z   42 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7521 (mp0)
REVERT: A  224 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7637 (tttm)
  outliers start: 17
  outliers final: 10
  residues processed: 108
  average time/residue: 0.2095
  time to fit residues: 31.1050
Evaluate side-chains
  108 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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 Y residue  213 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0870
   chunk 27 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0570
   chunk 86 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.8078

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.170012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.135377 restraints weight = 9405.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.19
r_work: 0.3161 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8235  Z= 0.179
  Angle     :  0.486   8.439  11171  Z= 0.255
  Chirality :  0.041   0.134   1284
  Planarity :  0.004   0.040   1417
  Dihedral  :  3.850  15.840   1134
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.89 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.27), residues: 1027
  helix:  2.42 (0.27), residues: 382
  sheet:  0.32 (0.35), residues: 217
  loop : -0.66 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 234 
 HIS   0.007   0.001   HIS X 357 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.013   0.001   TYR A 281 
 ARG   0.001   0.000   ARG X 347 

*********************** 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
  106 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.876 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8159 (ttt-90)
REVERT: Y   78 LYS cc_start: 0.9214 (tppt) cc_final: 0.8970 (tppt)
REVERT: Y  175 GLN cc_start: 0.8109 (mp10) cc_final: 0.7715 (mp10)
REVERT: Z   42 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7412 (mp0)
REVERT: A  224 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7671 (tttm)
  outliers start: 12
  outliers final: 8
  residues processed: 99
  average time/residue: 0.2393
  time to fit residues: 31.6830
Evaluate side-chains
  99 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  118 ASP
Chi-restraints excluded: chain Y residue  270 ILE
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 44 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0370
   chunk 89 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0980
   chunk 21 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.5460

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.167054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.135565 restraints weight = 9221.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.85
r_work: 0.3321 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8235  Z= 0.144
  Angle     :  0.456   8.188  11171  Z= 0.241
  Chirality :  0.040   0.132   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.701  15.610   1134
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.65 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1027
  helix:  2.55 (0.28), residues: 382
  sheet:  0.25 (0.35), residues: 220
  loop : -0.64 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP X 234 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.011   0.001   PHE N 108 
 TYR   0.012   0.001   TYR A 281 
 ARG   0.001   0.000   ARG Y 197 

*********************** 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
  105 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.844 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8291 (ttt-90)
REVERT: Y   96 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7631 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8225 (mp10) cc_final: 0.7761 (mp10)
REVERT: Y  214 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7381 (mtm-85)
REVERT: Z   42 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7538 (mp0)
REVERT: A  224 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7636 (tttp)
  outliers start: 15
  outliers final: 8
  residues processed: 102
  average time/residue: 0.2340
  time to fit residues: 31.8492
Evaluate side-chains
  99 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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   96 ARG
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  229 ILE
Chi-restraints excluded: chain A residue  281 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 83 optimal weight:    0.4980
   chunk 0 optimal weight:    7.9990
   chunk 76 optimal weight:    0.0770
   chunk 37 optimal weight:    0.0870
   chunk 3 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0060
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.3332

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.168972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.136238 restraints weight = 9300.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.08
r_work: 0.3232 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8235  Z= 0.124
  Angle     :  0.458  11.949  11171  Z= 0.237
  Chirality :  0.040   0.130   1284
  Planarity :  0.003   0.039   1417
  Dihedral  :  3.577  15.260   1134
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.27), residues: 1027
  helix:  2.61 (0.28), residues: 382
  sheet:  0.32 (0.35), residues: 220
  loop : -0.63 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP X 234 
 HIS   0.004   0.000   HIS X 357 
 PHE   0.010   0.001   PHE Y 241 
 TYR   0.014   0.001   TYR A 253 
 ARG   0.001   0.000   ARG Y 214 

*********************** 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
  109 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.957 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8312 (ttt-90)
REVERT: X  211 LYS cc_start: 0.8589 (mttm) cc_final: 0.8327 (mtpt)
REVERT: Y   96 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7620 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8210 (mp10) cc_final: 0.7735 (mp10)
REVERT: Y  294 CYS cc_start: 0.8550 (m) cc_final: 0.8191 (t)
REVERT: Z   42 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7529 (mp0)
REVERT: A  224 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7639 (tttp)
  outliers start: 15
  outliers final: 11
  residues processed: 104
  average time/residue: 0.2497
  time to fit residues: 34.4504
Evaluate side-chains
  104 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
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   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  102 MET
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  288 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   chunk 10 optimal weight:    0.4980
   chunk 88 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.6988

-------------------------------------------------------------------------------
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 = 0.3806 r_free = 0.3806 target = 0.160469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.127689 restraints weight = 9348.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.98
r_work: 0.2913 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   8235  Z= 0.478
  Angle     :  0.660   8.370  11171  Z= 0.342
  Chirality :  0.047   0.146   1284
  Planarity :  0.005   0.039   1417
  Dihedral  :  4.388  15.938   1134
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.99 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1027
  helix:  2.00 (0.27), residues: 385
  sheet:  0.33 (0.35), residues: 223
  loop : -0.96 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP N  47 
 HIS   0.015   0.001   HIS X 357 
 PHE   0.027   0.002   PHE N 108 
 TYR   0.019   0.002   TYR X 339 
 ARG   0.003   0.000   ARG Y 137 

*********************** 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
  121 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.889 
Fit side-chains
REVERT: Y   96 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7601 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8184 (mp10) cc_final: 0.7583 (mp10)
REVERT: Z   42 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7128 (mt-10)
REVERT: A  162 PHE cc_start: 0.6819 (t80) cc_final: 0.6524 (t80)
REVERT: A  224 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7600 (tttm)
  outliers start: 18
  outliers final: 12
  residues processed: 113
  average time/residue: 0.2261
  time to fit residues: 34.7846
Evaluate side-chains
  116 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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   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  327 VAL
Chi-restraints excluded: chain Z residue   42 GLU
Chi-restraints excluded: chain A residue  207 THR
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 1 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.163165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.131002 restraints weight = 9352.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.09
r_work: 0.3186 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8235  Z= 0.293
  Angle     :  0.560   9.571  11171  Z= 0.291
  Chirality :  0.043   0.140   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  4.235  21.342   1134
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.93 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.26), residues: 1027
  helix:  2.08 (0.27), residues: 385
  sheet:  0.31 (0.35), residues: 223
  loop : -0.91 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N  47 
 HIS   0.010   0.001   HIS X 357 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.016   0.002   TYR A 219 
 ARG   0.003   0.000   ARG Y 197 

*********************** 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
  115 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.850 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8258 (ttt-90)
REVERT: Y   96 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7617 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8287 (mp10) cc_final: 0.7798 (mp10)
REVERT: Y  186 ASP cc_start: 0.8513 (m-30) cc_final: 0.8210 (m-30)
REVERT: Z   42 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7432 (mp0)
REVERT: A  162 PHE cc_start: 0.6867 (t80) cc_final: 0.6585 (t80)
REVERT: A  224 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7608 (tttm)
  outliers start: 15
  outliers final: 12
  residues processed: 107
  average time/residue: 0.2273
  time to fit residues: 32.4560
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  : 0.912 
-------------------------------------------------------------------------------
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  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  207 THR
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 38 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 87 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.163917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.131683 restraints weight = 9493.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.00
r_work: 0.3233 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8235  Z= 0.241
  Angle     :  0.543  10.628  11171  Z= 0.282
  Chirality :  0.042   0.137   1284
  Planarity :  0.004   0.038   1417
  Dihedral  :  4.151  22.522   1134
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1027
  helix:  2.19 (0.27), residues: 385
  sheet:  0.40 (0.35), residues: 221
  loop : -0.90 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N  47 
 HIS   0.008   0.001   HIS X 357 
 PHE   0.016   0.001   PHE N 108 
 TYR   0.015   0.001   TYR A 219 
 ARG   0.006   0.000   ARG Y 197 

*********************** 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
  113 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.863 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8261 (ttt-90)
REVERT: Y   96 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7649 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8303 (mp10) cc_final: 0.7815 (mp10)
REVERT: Z   42 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7523 (mp0)
REVERT: A  224 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7619 (tttm)
  outliers start: 16
  outliers final: 14
  residues processed: 106
  average time/residue: 0.2501
  time to fit residues: 35.4124
Evaluate side-chains
  113 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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   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  207 THR
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  288 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 22 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 47 optimal weight:    0.4980
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.169409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.133757 restraints weight = 9446.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.84
r_work: 0.3150 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8235  Z= 0.175
  Angle     :  0.495   7.818  11171  Z= 0.259
  Chirality :  0.041   0.133   1284
  Planarity :  0.004   0.038   1417
  Dihedral  :  3.954  24.643   1134
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.28 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.27), residues: 1027
  helix:  2.35 (0.27), residues: 386
  sheet:  0.39 (0.36), residues: 218
  loop : -0.79 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP N  47 
 HIS   0.006   0.001   HIS X 357 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.013   0.001   TYR A 219 
 ARG   0.006   0.000   ARG Y 197 

********************** 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
  106 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 1.061 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8285 (ttt-90)
REVERT: Y   96 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7609 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8207 (mp10) cc_final: 0.7645 (mp10)
REVERT: Z   42 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7498 (mp0)
REVERT: A  224 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7527 (tttm)
  outliers start: 16
  outliers final: 14
  residues processed: 99
  average time/residue: 0.2493
  time to fit residues: 33.0254
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  : 0.959 
-------------------------------------------------------------------------------
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   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  207 THR
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  288 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.167139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.131043 restraints weight = 9510.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.87
r_work: 0.3112 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8235  Z= 0.253
  Angle     :  0.539   8.227  11171  Z= 0.281
  Chirality :  0.043   0.137   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  4.100  24.449   1134
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.74 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.27), residues: 1027
  helix:  2.31 (0.27), residues: 384
  sheet:  0.45 (0.35), residues: 215
  loop : -0.87 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N  47 
 HIS   0.009   0.001   HIS X 357 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.016   0.002   TYR A 219 
 ARG   0.006   0.000   ARG Y 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4518.90 seconds
wall clock time: 80 minutes 40.82 seconds (4840.82 seconds total)