Starting phenix.real_space_refine
on Wed Mar 12 15:00:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uxv_42786/03_2025/8uxv_42786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uxv_42786/03_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_42786/03_2025/8uxv_42786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uxv_42786/03_2025/8uxv_42786.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uxv_42786/03_2025/8uxv_42786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uxv_42786/03_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-5624/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: 5.18, per 1000 atoms: 0.64
  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.09
  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: 2.45

  Time building geometry restraints manager: 2.48 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:             1.040
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.030
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.710
-------------------------------------------------------------------------------
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  : 0.884 
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: 0.2310
  time to fit residues: 35.4250
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  : 0.849 
-------------------------------------------------------------------------------
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 = 9302.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.24
r_work: 0.3143 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
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  : 0.953 
Fit side-chains
REVERT: Y  175 GLN cc_start: 0.8209 (mp10) cc_final: 0.7802 (mp10)
REVERT: Z   51 LEU cc_start: 0.8820 (tp) cc_final: 0.8557 (tp)
REVERT: A  224 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7626 (tttm)
  outliers start: 10
  outliers final: 5
  residues processed: 112
  average time/residue: 0.2071
  time to fit residues: 31.7353
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  : 0.961 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   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:    8.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.163429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.131052 restraints weight = 9336.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.04
r_work: 0.3235 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8235  Z= 0.313
  Angle     :  0.570   9.930  11171  Z= 0.297
  Chirality :  0.044   0.139   1284
  Planarity :  0.004   0.042   1417
  Dihedral  :  4.162  17.125   1134
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.13 %
    Favored  : 88.76 %
  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:  0.81 (0.26), residues: 1027
  helix:  2.21 (0.27), residues: 379
  sheet:  0.28 (0.35), residues: 223
  loop : -0.87 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP N  47 
 HIS   0.012   0.001   HIS X 357 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.015   0.002   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
  118 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.918 
Fit side-chains
REVERT: Y  175 GLN cc_start: 0.8297 (mp10) cc_final: 0.7859 (mp10)
REVERT: Y  186 ASP cc_start: 0.8524 (m-30) cc_final: 0.8210 (m-30)
REVERT: Z   42 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7581 (mp0)
REVERT: A  224 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7652 (tttm)
  outliers start: 18
  outliers final: 11
  residues processed: 108
  average time/residue: 0.2108
  time to fit residues: 31.2008
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  : 0.809 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    0.0270
   chunk 73 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0070
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.5256

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.171590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.137256 restraints weight = 9404.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.19
r_work: 0.3216 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8235  Z= 0.149
  Angle     :  0.464   8.958  11171  Z= 0.246
  Chirality :  0.040   0.133   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.796  16.217   1134
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.24 %
    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:  1.04 (0.27), residues: 1027
  helix:  2.41 (0.27), residues: 386
  sheet:  0.35 (0.36), residues: 213
  loop : -0.76 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 234 
 HIS   0.006   0.001   HIS X 357 
 PHE   0.011   0.001   PHE Y 241 
 TYR   0.012   0.001   TYR A 281 
 ARG   0.002   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
  105 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.861 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8155 (ttt-90)
REVERT: Y   14 LEU cc_start: 0.6283 (mp) cc_final: 0.6063 (mp)
REVERT: Y   78 LYS cc_start: 0.9195 (tppt) cc_final: 0.8963 (tppt)
REVERT: Y  175 GLN cc_start: 0.8122 (mp10) cc_final: 0.7726 (mp10)
REVERT: Y  214 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7219 (mtm-85)
REVERT: Z   42 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7418 (mp0)
REVERT: A  224 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7677 (tttm)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2189
  time to fit residues: 29.6463
Evaluate side-chains
  98 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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:    3.9990
   chunk 6 optimal weight:    0.0980
   chunk 89 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 71 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.170662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.136325 restraints weight = 9374.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.24
r_work: 0.3157 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8235  Z= 0.166
  Angle     :  0.466   7.989  11171  Z= 0.248
  Chirality :  0.041   0.135   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.749  15.650   1134
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.65 %
    Favored  : 85.71 %
  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:  1.14 (0.27), residues: 1027
  helix:  2.50 (0.27), residues: 386
  sheet:  0.29 (0.35), residues: 218
  loop : -0.64 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP X 234 
 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   0.002   0.000   ARG Y 214 

*********************** 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: 14
    poor density    : 91
  time to evaluate  : 0.815 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8319 (ttt-90)
REVERT: Y   14 LEU cc_start: 0.6448 (mp) cc_final: 0.6216 (mp)
REVERT: Y   96 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7662 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8187 (mp10) cc_final: 0.7700 (mp10)
REVERT: Z   42 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7498 (mp0)
REVERT: A  224 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7654 (tttm)
  outliers start: 14
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2301
  time to fit residues: 31.0272
Evaluate side-chains
  98 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 76 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0670
   chunk 3 optimal weight:    4.9990
   chunk 38 optimal weight:    0.1980
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.9122

-------------------------------------------------------------------------------
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 = 0.169820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.135335 restraints weight = 9384.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.26
r_work: 0.3154 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1329

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= 0.195
  Angle     :  0.483   7.634  11171  Z= 0.256
  Chirality :  0.041   0.135   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.804  15.427   1134
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.75 %
    Favored  : 83.72 %
  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:  1.12 (0.27), residues: 1027
  helix:  2.52 (0.27), residues: 382
  sheet:  0.31 (0.35), residues: 218
  loop : -0.68 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N  47 
 HIS   0.007   0.001   HIS X 357 
 PHE   0.015   0.001   PHE N 108 
 TYR   0.015   0.001   TYR A 253 
 ARG   0.002   0.000   ARG Y 197 

*********************** 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
  104 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.841 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8262 (ttt-90)
REVERT: Y   14 LEU cc_start: 0.6267 (mp) cc_final: 0.6057 (mp)
REVERT: Y   96 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7499 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8107 (mp10) cc_final: 0.7703 (mp10)
REVERT: Z   42 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7388 (mp0)
REVERT: A  224 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7623 (tttm)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2273
  time to fit residues: 30.0764
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  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain X residue  224 VAL
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   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  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 40 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0670
   chunk 16 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.0124

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.162336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.129668 restraints weight = 9313.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.00
r_work: 0.3227 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   8235  Z= 0.365
  Angle     :  0.583   7.317  11171  Z= 0.306
  Chirality :  0.045   0.142   1284
  Planarity :  0.005   0.041   1417
  Dihedral  :  4.201  15.506   1134
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.99 %
    Favored  : 83.26 %
  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:  0.82 (0.26), residues: 1027
  helix:  2.22 (0.27), residues: 385
  sheet:  0.29 (0.35), residues: 223
  loop : -0.91 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP N  47 
 HIS   0.012   0.001   HIS X 357 
 PHE   0.022   0.002   PHE N 108 
 TYR   0.017   0.002   TYR A 219 
 ARG   0.003   0.000   ARG A 141 

*********************** 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
  114 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 1.511 
Fit side-chains
REVERT: Y   14 LEU cc_start: 0.6642 (mp) cc_final: 0.6373 (mp)
REVERT: Y   96 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7676 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8327 (mp10) cc_final: 0.7818 (mp10)
REVERT: Y  186 ASP cc_start: 0.8562 (m-30) cc_final: 0.8233 (m-30)
REVERT: Z   42 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7391 (mt-10)
REVERT: A  162 PHE cc_start: 0.6948 (t80) cc_final: 0.6660 (t80)
REVERT: A  224 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7680 (tttm)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2647
  time to fit residues: 38.7987
Evaluate side-chains
  109 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   65 THR
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  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:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0470
   overall best weight:    0.8882

-------------------------------------------------------------------------------
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 = 0.3886 r_free = 0.3886 target = 0.168620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.132718 restraints weight = 9438.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.84
r_work: 0.3139 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8235  Z= 0.192
  Angle     :  0.497   7.485  11171  Z= 0.263
  Chirality :  0.041   0.136   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.993  15.871   1134
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.25
  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 (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:  0.97 (0.27), residues: 1027
  helix:  2.41 (0.27), residues: 381
  sheet:  0.32 (0.35), residues: 217
  loop : -0.82 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP N  47 
 HIS   0.007   0.001   HIS X 357 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.014   0.001   TYR A 219 
 ARG   0.002   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
  104 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.965 
Fit side-chains
REVERT: N   19 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8280 (ttt-90)
REVERT: Y   14 LEU cc_start: 0.6504 (mp) cc_final: 0.6272 (mp)
REVERT: Y   96 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7641 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8198 (mp10) cc_final: 0.7635 (mp10)
REVERT: Z   42 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7476 (mp0)
REVERT: A  224 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7500 (tttm)
  outliers start: 13
  outliers final: 11
  residues processed: 99
  average time/residue: 0.2370
  time to fit residues: 31.0504
Evaluate side-chains
  103 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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
Chi-restraints excluded: chain A residue  288 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0970
   chunk 67 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.167556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.131513 restraints weight = 9564.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.86
r_work: 0.3223 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8235  Z= 0.242
  Angle     :  0.527  10.676  11171  Z= 0.276
  Chirality :  0.042   0.137   1284
  Planarity :  0.004   0.040   1417
  Dihedral  :  4.024  15.399   1134
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.81 %
    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 (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:  0.97 (0.27), residues: 1027
  helix:  2.37 (0.27), residues: 382
  sheet:  0.47 (0.36), residues: 212
  loop : -0.87 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N  47 
 HIS   0.008   0.001   HIS X 357 
 PHE   0.017   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
  105 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.979 
Fit side-chains
REVERT: Y   96 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7602 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8243 (mp10) cc_final: 0.7688 (mp10)
REVERT: Z   42 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7385 (mp0)
REVERT: A  224 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7486 (tttm)
  outliers start: 13
  outliers final: 11
  residues processed: 100
  average time/residue: 0.2637
  time to fit residues: 34.4595
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  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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
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:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.170044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.134489 restraints weight = 9421.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.84
r_work: 0.3162 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
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      :  0.003   0.032   8235  Z= 0.166
  Angle     :  0.487   8.609  11171  Z= 0.257
  Chirality :  0.041   0.133   1284
  Planarity :  0.004   0.039   1417
  Dihedral  :  3.857  15.439   1134
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.69 %
    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 (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:  1.11 (0.27), residues: 1027
  helix:  2.49 (0.28), residues: 383
  sheet:  0.51 (0.36), residues: 213
  loop : -0.78 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 234 
 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
  101 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 1.058 
Fit side-chains
REVERT: Y   96 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7596 (tmm-80)
REVERT: Y  175 GLN cc_start: 0.8193 (mp10) cc_final: 0.7639 (mp10)
REVERT: Z   42 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7476 (mp0)
REVERT: A  224 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7523 (tttm)
  outliers start: 14
  outliers final: 10
  residues processed: 95
  average time/residue: 0.2606
  time to fit residues: 32.8363
Evaluate side-chains
  96 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0770
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.3940

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.164179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.131679 restraints weight = 9346.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.00
r_work: 0.3255 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8235  Z= 0.268
  Angle     :  0.549  10.554  11171  Z= 0.286
  Chirality :  0.043   0.138   1284
  Planarity :  0.004   0.040   1417
  Dihedral  :  4.068  15.543   1134
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.04 %
    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:  1.00 (0.27), residues: 1027
  helix:  2.38 (0.27), residues: 382
  sheet:  0.56 (0.36), residues: 210
  loop : -0.87 (0.28), residues: 435

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   0.018   0.001   PHE N 108 
 TYR   0.017   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: 4578.91 seconds
wall clock time: 79 minutes 56.48 seconds (4796.48 seconds total)