Starting phenix.real_space_refine
on Sun May  3 14:23:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wd9_65886/05_2026/9wd9_65886_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wd9_65886/05_2026/9wd9_65886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wd9_65886/05_2026/9wd9_65886_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wd9_65886/05_2026/9wd9_65886_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wd9_65886/05_2026/9wd9_65886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wd9_65886/05_2026/9wd9_65886.map"
  }
  resolution = 2.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.043
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: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    4282      2.51       5
     N    1161      2.21       5
     O    1314      1.98       5
     H    6530      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13344
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "a"
      Number of atoms: 6667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 6667
          Classifications: {'peptide': 431}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 6611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 6611
          Classifications: {'peptide': 429}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409}
    Chain: "a"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "b"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.91, per 1000 atoms: 0.22
  Number of scatterers: 13344
  At special positions: 0
  Unit cell: (74.5446, 77.4117, 112.773, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      49     16.00
     P       6     15.00
     Mg      2     11.99
     O    1314      8.00
     N    1161      7.00
     C    4282      6.00
     H    6530      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.14
  Conformation dependent library (CDL) restraints added in 446.6 milliseconds
  

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1594

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      53.1% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'a' and resid 10 through 28
      removed outlier: 3.667A  pdb=" N   ALA a  19 " --> pdb=" O   GLN a  15 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 47 through 51
      removed outlier: 3.796A  pdb=" N   THR a  51 " --> pdb=" O   SER a  48 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 72 through 79
      removed outlier: 3.655A  pdb=" N   GLU a  77 " --> pdb=" O   THR a  73 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   VAL a  78 " --> pdb=" O   VAL a  74 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 88 through 90
      No H-bonds generated for 'chain 'a' and resid 88 through 90'
    Processing helix  chain 'a' and resid 102 through 108
    Processing helix  chain 'a' and resid 110 through 113
    Processing helix  chain 'a' and resid 114 through 128
    Processing helix  chain 'a' and resid 144 through 161
      removed outlier: 4.297A  pdb=" N   THR a 150 " --> pdb=" O   GLY a 146 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL a 159 " --> pdb=" O   GLU a 155 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 182 through 190
    Processing helix  chain 'a' and resid 190 through 197
    Processing helix  chain 'a' and resid 205 through 216
    Processing helix  chain 'a' and resid 223 through 240
      removed outlier: 3.613A  pdb=" N   LEU a 230 " --> pdb=" O   ASN a 226 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 241 through 243
      No H-bonds generated for 'chain 'a' and resid 241 through 243'
    Processing helix  chain 'a' and resid 251 through 258
    Processing helix  chain 'a' and resid 277 through 282
      removed outlier: 4.089A  pdb=" N   TYR a 282 " --> pdb=" O   ALA a 278 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 287 through 295
    Processing helix  chain 'a' and resid 306 through 310
    Processing helix  chain 'a' and resid 324 through 336
    Processing helix  chain 'a' and resid 384 through 401
      removed outlier: 3.812A  pdb=" N   TRP a 388 " --> pdb=" O   ILE a 384 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS a 394 " --> pdb=" O   ARG a 390 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LYS a 401 " --> pdb=" O   LEU a 397 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 404 through 410
      removed outlier: 4.148A  pdb=" N   TYR a 408 " --> pdb=" O   PHE a 404 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 415 through 435
      removed outlier: 4.258A  pdb=" N   SER a 419 " --> pdb=" O   GLU a 415 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 10 through 28
    Processing helix  chain 'b' and resid 40 through 45
      removed outlier: 3.516A  pdb=" N   LEU b  44 " --> pdb=" O   ASP b  41 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 46 through 49
    Processing helix  chain 'b' and resid 70 through 78
      removed outlier: 3.646A  pdb=" N   ASP b  74 " --> pdb=" O   PRO b  70 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 81 through 85
      removed outlier: 3.538A  pdb=" N   LEU b  84 " --> pdb=" O   PHE b  81 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE b  85 " --> pdb=" O   GLY b  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'b' and resid 81 through 85'
    Processing helix  chain 'b' and resid 86 through 88
      No H-bonds generated for 'chain 'b' and resid 86 through 88'
    Processing helix  chain 'b' and resid 100 through 106
    Processing helix  chain 'b' and resid 107 through 126
      removed outlier: 3.912A  pdb=" N   GLU b 111 " --> pdb=" O   THR b 107 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ASP b 114 " --> pdb=" O   ALA b 110 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   SER b 115 " --> pdb=" O   GLU b 111 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL b 119 " --> pdb=" O   SER b 115 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN b 126 " --> pdb=" O   LYS b 122 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 145 through 159
      removed outlier: 3.504A  pdb=" N   GLU b 158 " --> pdb=" O   LYS b 154 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 180 through 196
      removed outlier: 4.406A  pdb=" N   HIS b 190 " --> pdb=" O   THR b 186 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   GLN b 191 " --> pdb=" O   LEU b 187 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   THR b 196 " --> pdb=" O   LEU b 192 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 203 through 214
    Processing helix  chain 'b' and resid 221 through 237
      removed outlier: 3.892A  pdb=" N   THR b 237 " --> pdb=" O   MET b 233 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 237 through 242
      removed outlier: 3.850A  pdb=" N   ARG b 241 " --> pdb=" O   THR b 237 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 249 through 258
    Processing helix  chain 'b' and resid 278 through 282
      removed outlier: 3.528A  pdb=" N   ARG b 282 " --> pdb=" O   GLN b 279 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 285 through 294
    Processing helix  chain 'b' and resid 295 through 299
      removed outlier: 3.674A  pdb=" N   MET b 299 " --> pdb=" O   ALA b 296 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 304 through 308
    Processing helix  chain 'b' and resid 322 through 337
      removed outlier: 3.680A  pdb=" N   GLN b 334 " --> pdb=" O   MET b 330 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 338 through 341
      removed outlier: 3.578A  pdb=" N   PHE b 341 " --> pdb=" O   SER b 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'b' and resid 338 through 341'
    Processing helix  chain 'b' and resid 374 through 390
      removed outlier: 3.707A  pdb=" N   PHE b 378 " --> pdb=" O   ILE b 374 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE b 381 " --> pdb=" O   LEU b 377 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 394 through 400
      removed outlier: 4.320A  pdb=" N   TYR b 398 " --> pdb=" O   PHE b 394 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 404 through 425
      removed outlier: 4.039A  pdb=" N   PHE b 408 " --> pdb=" O   ASP b 404 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR b 409 " --> pdb=" O   GLU b 405 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR b 425 " --> pdb=" O   GLU b 421 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'a' and resid 92 through 94
      removed outlier: 8.071A  pdb=" N   ILE a  93 " --> pdb=" O   ALA a  65 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE a  67 " --> pdb=" O   ILE a  93 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   VAL a  66 " --> pdb=" O   CYS a   4 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   SER a   6 " --> pdb=" O   VAL a  66 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   VAL a  68 " --> pdb=" O   SER a   6 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   HIS a   8 " --> pdb=" O   VAL a  68 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   SER a 140 " --> pdb=" O   VAL a   9 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   PHE a 135 " --> pdb=" O   LEU a 167 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   PHE a 169 " --> pdb=" O   PHE a 135 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   VAL a 137 " --> pdb=" O   PHE a 169 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ILE a 171 " --> pdb=" O   VAL a 137 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   HIS a 139 " --> pdb=" O   ILE a 171 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LYS a 166 " --> pdb=" O   CYS a 200 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   PHE a 202 " --> pdb=" O   LYS a 166 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLU a 168 " --> pdb=" O   PHE a 202 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL a 204 " --> pdb=" O   GLU a 168 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   SER a 170 " --> pdb=" O   VAL a 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 53 through 56
    Processing sheet with id=AA3, first strand: chain 'a' and resid 269 through 273
      removed outlier: 6.664A  pdb=" N   ALA a 374 " --> pdb=" O   TYR a 319 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   TYR a 319 " --> pdb=" O   ALA a 374 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   CYS a 376 " --> pdb=" O   LEU a 317 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   LEU a 317 " --> pdb=" O   CYS a 376 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LEU a 378 " --> pdb=" O   CYS a 315 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   CYS a 315 " --> pdb=" O   LEU a 378 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ASN a 380 " --> pdb=" O   MET a 313 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'b' and resid 90 through 92
      removed outlier: 8.236A  pdb=" N   ILE b  91 " --> pdb=" O   ALA b  63 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU b  65 " --> pdb=" O   ILE b  91 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   ILE b  64 " --> pdb=" O   ILE b   4 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   HIS b   6 " --> pdb=" O   ILE b  64 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   VAL b  66 " --> pdb=" O   HIS b   6 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   GLN b   8 " --> pdb=" O   VAL b  66 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   GLU b   3 " --> pdb=" O   GLN b 131 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   PHE b 133 " --> pdb=" O   GLU b   3 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL b   5 " --> pdb=" O   PHE b 133 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   LEU b 135 " --> pdb=" O   VAL b   5 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE b   7 " --> pdb=" O   LEU b 135 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   HIS b 137 " --> pdb=" O   ILE b   7 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ALA b   9 " --> pdb=" O   HIS b 137 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   GLN b 131 " --> pdb=" O   ILE b 163 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   ASN b 165 " --> pdb=" O   GLN b 131 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   PHE b 133 " --> pdb=" O   ASN b 165 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   PHE b 167 " --> pdb=" O   PHE b 133 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LEU b 135 " --> pdb=" O   PHE b 167 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   VAL b 169 " --> pdb=" O   LEU b 135 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   HIS b 137 " --> pdb=" O   VAL b 169 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   MET b 164 " --> pdb=" O   GLU b 198 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   TYR b 200 " --> pdb=" O   MET b 164 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR b 166 " --> pdb=" O   TYR b 200 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ILE b 202 " --> pdb=" O   THR b 166 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   SER b 168 " --> pdb=" O   ILE b 202 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   THR b 199 " --> pdb=" O   PHE b 266 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   CYS b 201 " --> pdb=" O   PRO b 268 " (cutoff:3.500A)
      removed outlier: 10.829A  pdb=" N   PHE b 270 " --> pdb=" O   CYS b 201 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   PHE b 265 " --> pdb=" O   SER b 371 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   SER b 371 " --> pdb=" O   PHE b 265 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   SER b 364 " --> pdb=" O   PHE b 317 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   PHE b 317 " --> pdb=" O   SER b 364 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   THR b 366 " --> pdb=" O   THR b 315 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR b 315 " --> pdb=" O   THR b 366 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE b 368 " --> pdb=" O   VAL b 313 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL b 313 " --> pdb=" O   ILE b 368 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASN b 370 " --> pdb=" O   LEU b 311 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'b' and resid 51 through 54
      removed outlier: 3.725A  pdb=" N   LYS b  58 " --> pdb=" O   ALA b  54 " (cutoff:3.500A)

    293 hydrogen bonds defined for protein.
    840 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: 2.85

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        0.84 -     1.06: 6511
        1.06 -     1.29: 1168
        1.29 -     1.52: 3801
        1.52 -     1.74: 1938
        1.74 -     1.97: 80
  Bond restraints: 13498
  Sorted by residual:
  bond pdb=" O5' G2P b 501 "
       pdb=" PA  G2P b 501 "
    ideal  model  delta    sigma   weight residual
    1.656  1.858 -0.202 2.00e-02 2.50e+03 1.02e+02
  bond pdb=" C3A G2P b 501 "
       pdb=" PA  G2P b 501 "
    ideal  model  delta    sigma   weight residual
    1.818  1.683  0.135 2.00e-02 2.50e+03 4.54e+01
  bond pdb=" C3A G2P b 501 "
       pdb=" PB  G2P b 501 "
    ideal  model  delta    sigma   weight residual
    1.850  1.971 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" O3B G2P b 501 "
       pdb=" PG  G2P b 501 "
    ideal  model  delta    sigma   weight residual
    1.716  1.814 -0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" C5' G2P b 501 "
       pdb=" O5' G2P b 501 "
    ideal  model  delta    sigma   weight residual
    1.399  1.317  0.082 2.00e-02 2.50e+03 1.68e+01
  ... (remaining 13493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.25: 24272
        7.25 -    14.50: 13
       14.50 -    21.74: 3
       21.74 -    28.99: 1
       28.99 -    36.24: 3
  Bond angle restraints: 24292
  Sorted by residual:
  angle pdb=" N   PHE a  49 "
        pdb=" CA  PHE a  49 "
        pdb=" HA  PHE a  49 "
      ideal   model   delta    sigma   weight residual
     110.00   73.76   36.24 3.00e+00 1.11e-01 1.46e+02
  angle pdb=" C   PHE a  49 "
        pdb=" CA  PHE a  49 "
        pdb=" HA  PHE a  49 "
      ideal   model   delta    sigma   weight residual
     109.00   73.54   35.46 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" CB  PHE a  49 "
        pdb=" CA  PHE a  49 "
        pdb=" HA  PHE a  49 "
      ideal   model   delta    sigma   weight residual
     109.00   77.48   31.52 3.00e+00 1.11e-01 1.10e+02
  angle pdb=" PA  GTP a 501 "
        pdb=" O3A GTP a 501 "
        pdb=" PB  GTP a 501 "
      ideal   model   delta    sigma   weight residual
     120.50  143.64  -23.14 3.00e+00 1.11e-01 5.95e+01
  angle pdb=" O1A G2P b 501 "
        pdb=" PA  G2P b 501 "
        pdb=" O5' G2P b 501 "
      ideal   model   delta    sigma   weight residual
     109.23   88.15   21.08 3.00e+00 1.11e-01 4.94e+01
  ... (remaining 24287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.47: 6094
       30.47 -    60.95: 296
       60.95 -    91.42: 20
       91.42 -   121.89: 2
      121.89 -   152.37: 2
  Dihedral angle restraints: 6414
    sinusoidal: 3463
      harmonic: 2951
  Sorted by residual:
  dihedral pdb=" C8  GTP a 501 "
           pdb=" C1' GTP a 501 "
           pdb=" N9  GTP a 501 "
           pdb=" O4' GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -47.77  152.37     1      2.00e+01 2.50e-03 4.53e+01
  dihedral pdb=" O3A GTP a 501 "
           pdb=" O3B GTP a 501 "
           pdb=" PB  GTP a 501 "
           pdb=" PG  GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.79  179.37  124.43     1      2.00e+01 2.50e-03 3.76e+01
  dihedral pdb=" C5' GTP a 501 "
           pdb=" O5' GTP a 501 "
           pdb=" PA  GTP a 501 "
           pdb=" O3A GTP a 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -171.03 -119.70     1      2.00e+01 2.50e-03 3.59e+01
  ... (remaining 6411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 935
       0.071 -    0.141: 95
       0.141 -    0.212: 2
       0.212 -    0.282: 3
       0.282 -    0.353: 1
  Chirality restraints: 1036
  Sorted by residual:
  chirality pdb=" CA  PHE a  49 "
            pdb=" N   PHE a  49 "
            pdb=" C   PHE a  49 "
            pdb=" CB  PHE a  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" C2' G2P b 501 "
            pdb=" C1' G2P b 501 "
            pdb=" C3' G2P b 501 "
            pdb=" O2' G2P b 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.75    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C3' GTP a 501 "
            pdb=" C2' GTP a 501 "
            pdb=" C4' GTP a 501 "
            pdb=" O3' GTP a 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.72    0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 1033 not shown)

  Planarity restraints: 2028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' GTP a 501 "    0.025 2.00e-02 2.50e+03   1.04e-02 3.27e+00
        pdb=" C2  GTP a 501 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4  GTP a 501 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5  GTP a 501 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6  GTP a 501 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8  GTP a 501 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1  GTP a 501 "    0.006 2.00e-02 2.50e+03
        pdb=" N2  GTP a 501 "    0.002 2.00e-02 2.50e+03
        pdb=" N3  GTP a 501 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7  GTP a 501 "   -0.005 2.00e-02 2.50e+03
        pdb=" N9  GTP a 501 "   -0.015 2.00e-02 2.50e+03
        pdb=" O6  GTP a 501 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN a  31 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO a  32 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO a  32 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO a  32 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL a 324 "   -0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO a 325 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO a 325 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO a 325 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2025 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 2899
        2.31 -     2.88: 28945
        2.88 -     3.45: 33346
        3.45 -     4.03: 48367
        4.03 -     4.60: 71964
  Nonbonded interactions: 185521
  Sorted by model distance:
  nonbonded pdb=" H   PHE a  49 "
            pdb=" HA  PHE a  49 "
     model   vdw
     1.733 1.816
  nonbonded pdb=" HD1 HIS b   6 "
            pdb="HE21 GLN b 134 "
     model   vdw
     1.773 2.100
  nonbonded pdb="HH12 ARG b 276 "
            pdb="HE22 GLN b 280 "
     model   vdw
     1.843 2.100
  nonbonded pdb="HD22 ASN a 101 "
            pdb="HD21 ASN b 256 "
     model   vdw
     1.858 2.100
  nonbonded pdb=" H   GLU b 343 "
            pdb=" HG3 GLU b 343 "
     model   vdw
     1.860 2.270
  ... (remaining 185516 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:             8.600
  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:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
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      :  0.006   0.202   6968  Z= 0.284
  Angle     :  0.810  23.142   9465  Z= 0.349
  Chirality :  0.048   0.353   1036
  Planarity :  0.005   0.043   1229
  Dihedral  : 17.784 152.368   2567
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 17.19 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.28), residues: 854
  helix: -0.33 (0.26), residues: 374
  sheet:  0.08 (0.44), residues: 139
  loop : -0.70 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b 241 
 TYR   0.011   0.001   TYR b  59 
 PHE   0.012   0.002   PHE b  90 
 TRP   0.014   0.002   TRP a  21 
 HIS   0.005   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 6968)
  covalent geometry    : angle       0.80973 ( 9465)
  hydrogen bonds       : bond        0.29475 (  293)
  hydrogen bonds       : angle       7.10167 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.363 
Fit side-chains
REVERT: a   84 ARG cc_start: 0.8333 (ptp90) cc_final: 0.8124 (ptp90)
REVERT: a   97 GLU cc_start: 0.7943 (pt0) cc_final: 0.7641 (mt-10)
REVERT: a  279 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7527 (mp0)
REVERT: a  372 GLN cc_start: 0.8815 (mt0) cc_final: 0.8329 (mm110)
REVERT: a  414 GLU cc_start: 0.8368 (mp0) cc_final: 0.8084 (tm-30)
REVERT: b  118 ASP cc_start: 0.8243 (t70) cc_final: 0.7912 (m-30)
REVERT: b  164 MET cc_start: 0.9006 (tpp) cc_final: 0.8717 (tpp)
REVERT: b  175 VAL cc_start: 0.8888 (t) cc_final: 0.8495 (p)
REVERT: b  280 GLN cc_start: 0.8385 (mp10) cc_final: 0.8094 (mp10)
REVERT: b  288 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7599 (tp30)
REVERT: b  338 SER cc_start: 0.8232 (p) cc_final: 0.8019 (t)
  outliers start: 5
  outliers final: 5
  residues processed: 89
  average time/residue: 1.3023
  time to fit residues: 121.5004
Evaluate side-chains
  89 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain b residue   72 THR
Chi-restraints excluded: chain b residue  157 GLU
Chi-restraints excluded: chain b residue  333 ILE
Chi-restraints excluded: chain b residue  348 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
a  88 HIS
b 279 GLN
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.105552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.085647 restraints weight = 21333.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.98
r_work: 0.3033 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6968  Z= 0.145
  Angle     :  0.559   7.160   9465  Z= 0.304
  Chirality :  0.045   0.358   1036
  Planarity :  0.005   0.041   1229
  Dihedral  : 10.902 149.747    989
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.96 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.29), residues: 854
  helix:  1.06 (0.27), residues: 382
  sheet:  0.02 (0.41), residues: 152
  loop : -0.63 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a 422 
 TYR   0.007   0.001   TYR b  59 
 PHE   0.010   0.001   PHE b 294 
 TRP   0.016   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6968)
  covalent geometry    : angle       0.55870 ( 9465)
  hydrogen bonds       : bond        0.08218 (  293)
  hydrogen bonds       : angle       4.90630 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.353 
Fit side-chains
REVERT: a   97 GLU cc_start: 0.7709 (pt0) cc_final: 0.7353 (mt-10)
REVERT: a  279 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7396 (mp0)
REVERT: a  285 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7649 (mt0)
REVERT: a  372 GLN cc_start: 0.8726 (mt0) cc_final: 0.8130 (mm110)
REVERT: a  414 GLU cc_start: 0.8200 (mp0) cc_final: 0.7750 (tm-30)
REVERT: b  118 ASP cc_start: 0.7850 (t70) cc_final: 0.7470 (m-30)
REVERT: b  147 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8391 (ttt)
REVERT: b  164 MET cc_start: 0.8889 (tpp) cc_final: 0.8496 (tpp)
REVERT: b  175 VAL cc_start: 0.8766 (t) cc_final: 0.8312 (p)
REVERT: b  280 GLN cc_start: 0.8187 (mp10) cc_final: 0.7757 (mp10)
REVERT: b  288 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7342 (mm-30)
REVERT: b  330 MET cc_start: 0.8916 (mmp) cc_final: 0.8149 (mmp)
REVERT: b  338 SER cc_start: 0.7769 (p) cc_final: 0.7497 (t)
REVERT: b  377 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8275 (tp)
  outliers start: 12
  outliers final: 6
  residues processed: 98
  average time/residue: 1.2572
  time to fit residues: 129.3718
Evaluate side-chains
  95 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue  147 MET
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  377 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
b 279 GLN
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.106196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.085944 restraints weight = 21542.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.02
r_work: 0.3043 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6968  Z= 0.140
  Angle     :  0.533   6.970   9465  Z= 0.283
  Chirality :  0.045   0.358   1036
  Planarity :  0.004   0.040   1229
  Dihedral  : 10.281 151.898    981
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.69 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.29), residues: 854
  helix:  1.31 (0.27), residues: 382
  sheet:  0.08 (0.41), residues: 152
  loop : -0.67 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b 241 
 TYR   0.009   0.001   TYR b  59 
 PHE   0.012   0.001   PHE a 255 
 TRP   0.016   0.002   TRP a  21 
 HIS   0.005   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6968)
  covalent geometry    : angle       0.53277 ( 9465)
  hydrogen bonds       : bond        0.07142 (  293)
  hydrogen bonds       : angle       4.48604 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.631 
Fit side-chains
REVERT: a   97 GLU cc_start: 0.7715 (pt0) cc_final: 0.7362 (mt-10)
REVERT: a  279 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7387 (mp0)
REVERT: a  285 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7647 (mt0)
REVERT: a  372 GLN cc_start: 0.8730 (mt0) cc_final: 0.8123 (mm110)
REVERT: a  414 GLU cc_start: 0.8145 (mp0) cc_final: 0.7723 (tm-30)
REVERT: b   31 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8133 (p0)
REVERT: b  118 ASP cc_start: 0.7877 (t70) cc_final: 0.7407 (m-30)
REVERT: b  164 MET cc_start: 0.8903 (tpp) cc_final: 0.8507 (tpp)
REVERT: b  280 GLN cc_start: 0.8201 (mp10) cc_final: 0.7745 (mp10)
REVERT: b  288 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7288 (mm-30)
REVERT: b  330 MET cc_start: 0.8902 (mmp) cc_final: 0.8143 (mmp)
REVERT: b  338 SER cc_start: 0.7790 (p) cc_final: 0.7509 (t)
REVERT: b  377 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8230 (tp)
  outliers start: 16
  outliers final: 12
  residues processed: 103
  average time/residue: 1.2009
  time to fit residues: 130.5402
Evaluate side-chains
  101 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  340 THR
Chi-restraints excluded: chain a residue  349 THR
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue   31 ASP
Chi-restraints excluded: chain b residue   88 ASP
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  219 THR
Chi-restraints excluded: chain b residue  333 ILE
Chi-restraints excluded: chain b residue  348 ASN
Chi-restraints excluded: chain b residue  377 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
b 279 GLN
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.105911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085678 restraints weight = 21383.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.00
r_work: 0.3038 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6968  Z= 0.148
  Angle     :  0.541   7.052   9465  Z= 0.287
  Chirality :  0.045   0.357   1036
  Planarity :  0.004   0.041   1229
  Dihedral  : 10.265 153.623    981
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 0.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.73 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.29), residues: 854
  helix:  1.37 (0.27), residues: 382
  sheet:  0.22 (0.43), residues: 139
  loop : -0.69 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 241 
 TYR   0.010   0.001   TYR b  59 
 PHE   0.012   0.001   PHE a 255 
 TRP   0.015   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6968)
  covalent geometry    : angle       0.54108 ( 9465)
  hydrogen bonds       : bond        0.06920 (  293)
  hydrogen bonds       : angle       4.39490 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.365 
Fit side-chains
REVERT: a   97 GLU cc_start: 0.7713 (pt0) cc_final: 0.7373 (mt-10)
REVERT: a  279 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7375 (mp0)
REVERT: a  285 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (mt0)
REVERT: a  372 GLN cc_start: 0.8725 (mt0) cc_final: 0.8136 (mm110)
REVERT: a  414 GLU cc_start: 0.8142 (mp0) cc_final: 0.7728 (tm-30)
REVERT: b   31 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8165 (p0)
REVERT: b  118 ASP cc_start: 0.7896 (t70) cc_final: 0.7412 (m-30)
REVERT: b  147 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8508 (ttt)
REVERT: b  164 MET cc_start: 0.8909 (tpp) cc_final: 0.8515 (tpp)
REVERT: b  280 GLN cc_start: 0.8171 (mp10) cc_final: 0.7733 (mp10)
REVERT: b  288 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7312 (mm-30)
REVERT: b  309 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7848 (mtt90)
REVERT: b  330 MET cc_start: 0.8928 (mmp) cc_final: 0.8188 (mmp)
REVERT: b  338 SER cc_start: 0.7771 (p) cc_final: 0.7490 (t)
  outliers start: 23
  outliers final: 14
  residues processed: 106
  average time/residue: 1.2371
  time to fit residues: 137.6892
Evaluate side-chains
  102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   71 GLU
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  170 SER
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  194 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  340 THR
Chi-restraints excluded: chain a residue  349 THR
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue   31 ASP
Chi-restraints excluded: chain b residue  147 MET
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  309 ARG
Chi-restraints excluded: chain b residue  333 ILE
Chi-restraints excluded: chain b residue  348 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
b 279 GLN
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.107040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.087035 restraints weight = 21663.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.01
r_work: 0.3061 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6968  Z= 0.123
  Angle     :  0.514   6.650   9465  Z= 0.271
  Chirality :  0.044   0.357   1036
  Planarity :  0.004   0.039   1229
  Dihedral  :  9.871 151.112    981
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 0.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.28 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.29), residues: 854
  helix:  1.50 (0.27), residues: 383
  sheet:  0.19 (0.41), residues: 150
  loop : -0.67 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b 241 
 TYR   0.009   0.001   TYR b  59 
 PHE   0.012   0.001   PHE a 255 
 TRP   0.015   0.001   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6968)
  covalent geometry    : angle       0.51372 ( 9465)
  hydrogen bonds       : bond        0.06077 (  293)
  hydrogen bonds       : angle       4.22486 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: a   50 ASN cc_start: 0.8395 (m110) cc_final: 0.8104 (m-40)
REVERT: a   97 GLU cc_start: 0.7719 (pt0) cc_final: 0.7374 (mt-10)
REVERT: a  279 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7387 (mp0)
REVERT: a  285 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7975 (mt0)
REVERT: a  372 GLN cc_start: 0.8712 (mt0) cc_final: 0.8127 (mm110)
REVERT: a  414 GLU cc_start: 0.8119 (mp0) cc_final: 0.7697 (tm-30)
REVERT: a  420 GLU cc_start: 0.7922 (tt0) cc_final: 0.7705 (mt-10)
REVERT: b   31 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (p0)
REVERT: b  118 ASP cc_start: 0.7878 (t70) cc_final: 0.7403 (m-30)
REVERT: b  164 MET cc_start: 0.8913 (tpp) cc_final: 0.8544 (tpp)
REVERT: b  280 GLN cc_start: 0.8161 (mp10) cc_final: 0.7701 (mp10)
REVERT: b  288 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7280 (mm-30)
REVERT: b  309 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7808 (mtt90)
REVERT: b  330 MET cc_start: 0.8921 (mmp) cc_final: 0.8658 (mmp)
REVERT: b  333 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7999 (tp)
REVERT: b  338 SER cc_start: 0.7727 (p) cc_final: 0.7443 (t)
  outliers start: 19
  outliers final: 13
  residues processed: 106
  average time/residue: 1.2566
  time to fit residues: 139.7783
Evaluate side-chains
  106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  340 THR
Chi-restraints excluded: chain a residue  349 THR
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue   31 ASP
Chi-restraints excluded: chain b residue   72 THR
Chi-restraints excluded: chain b residue   88 ASP
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  219 THR
Chi-restraints excluded: chain b residue  303 CYS
Chi-restraints excluded: chain b residue  309 ARG
Chi-restraints excluded: chain b residue  333 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 14 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:
a  15 GLN
b 279 GLN
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.106787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.086645 restraints weight = 21546.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.01
r_work: 0.3053 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6968  Z= 0.132
  Angle     :  0.524   6.703   9465  Z= 0.275
  Chirality :  0.044   0.360   1036
  Planarity :  0.004   0.039   1229
  Dihedral  :  9.912 152.814    981
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 0.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.73 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.29), residues: 854
  helix:  1.50 (0.27), residues: 383
  sheet:  0.19 (0.41), residues: 150
  loop : -0.66 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b 241 
 TYR   0.009   0.001   TYR b  59 
 PHE   0.012   0.001   PHE a 255 
 TRP   0.014   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6968)
  covalent geometry    : angle       0.52410 ( 9465)
  hydrogen bonds       : bond        0.06267 (  293)
  hydrogen bonds       : angle       4.21225 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: a   50 ASN cc_start: 0.8418 (m110) cc_final: 0.8126 (m-40)
REVERT: a   97 GLU cc_start: 0.7720 (pt0) cc_final: 0.7356 (mt-10)
REVERT: a  279 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7375 (mp0)
REVERT: a  285 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7986 (mt0)
REVERT: a  372 GLN cc_start: 0.8722 (mt0) cc_final: 0.8136 (mm110)
REVERT: a  414 GLU cc_start: 0.8119 (mp0) cc_final: 0.7694 (tm-30)
REVERT: a  420 GLU cc_start: 0.7920 (tt0) cc_final: 0.7707 (mt-10)
REVERT: b   31 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8137 (p0)
REVERT: b  118 ASP cc_start: 0.7897 (t70) cc_final: 0.7417 (m-30)
REVERT: b  147 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8506 (ttt)
REVERT: b  164 MET cc_start: 0.8921 (tpp) cc_final: 0.8559 (tpp)
REVERT: b  175 VAL cc_start: 0.8841 (t) cc_final: 0.8382 (p)
REVERT: b  280 GLN cc_start: 0.8160 (mp10) cc_final: 0.7699 (mp10)
REVERT: b  288 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7299 (mm-30)
REVERT: b  309 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7811 (mtt90)
REVERT: b  330 MET cc_start: 0.8900 (mmp) cc_final: 0.8141 (mmp)
REVERT: b  333 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7997 (tp)
REVERT: b  338 SER cc_start: 0.7747 (p) cc_final: 0.7467 (t)
  outliers start: 22
  outliers final: 15
  residues processed: 107
  average time/residue: 1.2458
  time to fit residues: 139.9584
Evaluate side-chains
  108 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   71 GLU
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  170 SER
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  194 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  340 THR
Chi-restraints excluded: chain a residue  349 THR
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue   31 ASP
Chi-restraints excluded: chain b residue   72 THR
Chi-restraints excluded: chain b residue  147 MET
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  219 THR
Chi-restraints excluded: chain b residue  309 ARG
Chi-restraints excluded: chain b residue  333 ILE
Chi-restraints excluded: chain b residue  348 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.107237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.087300 restraints weight = 21584.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.00
r_work: 0.3061 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6968  Z= 0.121
  Angle     :  0.514   6.657   9465  Z= 0.269
  Chirality :  0.044   0.359   1036
  Planarity :  0.004   0.039   1229
  Dihedral  :  9.732 151.283    981
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 0.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.42 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 854
  helix:  1.55 (0.27), residues: 384
  sheet:  0.21 (0.41), residues: 150
  loop : -0.62 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b 241 
 TYR   0.009   0.001   TYR b  59 
 PHE   0.011   0.001   PHE a 255 
 TRP   0.014   0.001   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6968)
  covalent geometry    : angle       0.51395 ( 9465)
  hydrogen bonds       : bond        0.05851 (  293)
  hydrogen bonds       : angle       4.13160 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.282 
Fit side-chains
REVERT: a   50 ASN cc_start: 0.8413 (m110) cc_final: 0.8122 (m-40)
REVERT: a   97 GLU cc_start: 0.7752 (pt0) cc_final: 0.7399 (mt-10)
REVERT: a  279 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7395 (mp0)
REVERT: a  285 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7994 (mt0)
REVERT: a  372 GLN cc_start: 0.8723 (mt0) cc_final: 0.8131 (mm110)
REVERT: a  414 GLU cc_start: 0.8082 (mp0) cc_final: 0.7648 (tm-30)
REVERT: b   31 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8098 (p0)
REVERT: b  118 ASP cc_start: 0.7871 (t70) cc_final: 0.7392 (m-30)
REVERT: b  164 MET cc_start: 0.8912 (tpp) cc_final: 0.8547 (tpp)
REVERT: b  280 GLN cc_start: 0.8151 (mp10) cc_final: 0.7694 (mp10)
REVERT: b  288 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7351 (mm-30)
REVERT: b  309 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7785 (mtt90)
REVERT: b  330 MET cc_start: 0.8914 (mmp) cc_final: 0.8653 (mmp)
REVERT: b  333 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7999 (tp)
REVERT: b  338 SER cc_start: 0.7680 (p) cc_final: 0.7409 (t)
  outliers start: 20
  outliers final: 13
  residues processed: 108
  average time/residue: 1.2557
  time to fit residues: 142.4902
Evaluate side-chains
  105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  170 SER
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  340 THR
Chi-restraints excluded: chain a residue  349 THR
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue   31 ASP
Chi-restraints excluded: chain b residue   72 THR
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  219 THR
Chi-restraints excluded: chain b residue  309 ARG
Chi-restraints excluded: chain b residue  333 ILE
Chi-restraints excluded: chain b residue  348 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086612 restraints weight = 21390.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.99
r_work: 0.3053 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6968  Z= 0.136
  Angle     :  0.528   6.848   9465  Z= 0.277
  Chirality :  0.044   0.361   1036
  Planarity :  0.004   0.038   1229
  Dihedral  :  9.881 153.217    981
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.28 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 854
  helix:  1.51 (0.27), residues: 383
  sheet:  0.31 (0.42), residues: 143
  loop : -0.57 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b 241 
 TYR   0.009   0.001   TYR b  59 
 PHE   0.012   0.001   PHE a 255 
 TRP   0.014   0.002   TRP a  21 
 HIS   0.004   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6968)
  covalent geometry    : angle       0.52768 ( 9465)
  hydrogen bonds       : bond        0.06269 (  293)
  hydrogen bonds       : angle       4.18237 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: a   50 ASN cc_start: 0.8425 (m110) cc_final: 0.8130 (m-40)
REVERT: a   97 GLU cc_start: 0.7732 (pt0) cc_final: 0.7418 (mt-10)
REVERT: a  279 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7377 (mp0)
REVERT: a  285 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8020 (mt0)
REVERT: a  372 GLN cc_start: 0.8720 (mt0) cc_final: 0.8137 (mm110)
REVERT: a  414 GLU cc_start: 0.8061 (mp0) cc_final: 0.7641 (tm-30)
REVERT: b   31 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8133 (p0)
REVERT: b  118 ASP cc_start: 0.7913 (t70) cc_final: 0.7427 (m-30)
REVERT: b  147 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8518 (ttt)
REVERT: b  164 MET cc_start: 0.8941 (tpp) cc_final: 0.8584 (tpp)
REVERT: b  280 GLN cc_start: 0.8160 (mp10) cc_final: 0.7682 (mp10)
REVERT: b  288 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7344 (mm-30)
REVERT: b  309 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7795 (mtt90)
REVERT: b  330 MET cc_start: 0.8907 (mmp) cc_final: 0.8151 (mmp)
REVERT: b  333 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8002 (tp)
REVERT: b  338 SER cc_start: 0.7727 (p) cc_final: 0.7485 (t)
  outliers start: 22
  outliers final: 17
  residues processed: 104
  average time/residue: 1.2667
  time to fit residues: 138.2482
Evaluate side-chains
  106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   54 SER
Chi-restraints excluded: chain a residue   71 GLU
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  170 SER
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  255 PHE
Chi-restraints excluded: chain a residue  285 GLN
Chi-restraints excluded: chain a residue  340 THR
Chi-restraints excluded: chain a residue  349 THR
Chi-restraints excluded: chain a residue  435 VAL
Chi-restraints excluded: chain b residue   31 ASP
Chi-restraints excluded: chain b residue   72 THR
Chi-restraints excluded: chain b residue   88 ASP
Chi-restraints excluded: chain b residue  147 MET
Chi-restraints excluded: chain b residue  166 THR
Chi-restraints excluded: chain b residue  168 SER
Chi-restraints excluded: chain b residue  219 THR
Chi-restraints excluded: chain b residue  232 THR
Chi-restraints excluded: chain b residue  303 CYS
Chi-restraints excluded: chain b residue  309 ARG
Chi-restraints excluded: chain b residue  333 ILE
Chi-restraints excluded: chain b residue  348 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0060
   chunk 68 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   chunk 4 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0670
   chunk 34 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0050
   overall best weight:    0.2146

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

Flipped N/Q/H residues before XYZ refinement:
b 347 ASN
b 416 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.111842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.092010 restraints weight = 21658.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.03
r_work: 0.3139 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6968  Z= 0.093
  Angle     :  0.475   6.481   9465  Z= 0.246
  Chirality :  0.042   0.355   1036
  Planarity :  0.004   0.037   1229
  Dihedral  :  8.921 144.123    981
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 0.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 17.33 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.29), residues: 854
  helix:  1.81 (0.27), residues: 385
  sheet:  0.30 (0.41), residues: 150
  loop : -0.49 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a  64 
 TYR   0.005   0.001   TYR a 210 
 PHE   0.008   0.001   PHE a 255 
 TRP   0.015   0.001   TRP a  21 
 HIS   0.002   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 6968)
  covalent geometry    : angle       0.47523 ( 9465)
  hydrogen bonds       : bond        0.04263 (  293)
  hydrogen bonds       : angle       3.81998 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.253 
Fit side-chains
REVERT: a   50 ASN cc_start: 0.8342 (m110) cc_final: 0.8060 (m-40)
REVERT: a   97 GLU cc_start: 0.7648 (pt0) cc_final: 0.7315 (mt-10)
REVERT: a  193 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8194 (t)
REVERT: a  279 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7433 (mp0)
REVERT: a  372 GLN cc_start: 0.8694 (mt0) cc_final: 0.8111 (mm110)
REVERT: a  414 GLU cc_start: 0.8016 (mp0) cc_final: 0.7570 (tm-30)
REVERT: b  118 ASP cc_start: 0.7828 (t70) cc_final: 0.7384 (m-30)
REVERT: b  164 MET cc_start: 0.8904 (tpp) cc_final: 0.8511 (tpp)
REVERT: b  213 ARG cc_start: 0.8312 (mtm180) cc_final: 0.8059 (mtm-85)
REVERT: b  280 GLN cc_start: 0.8154 (mp10) cc_final: 0.7694 (mp10)
REVERT: b  288 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7274 (mm-30)
REVERT: b  336 LYS cc_start: 0.7447 (mptm) cc_final: 0.7205 (mppt)
REVERT: b  338 SER cc_start: 0.7307 (p) cc_final: 0.7066 (t)
  outliers start: 8
  outliers final: 3
  residues processed: 100
  average time/residue: 1.2450
  time to fit residues: 130.6960
Evaluate side-chains
  93 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  170 SER
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  349 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
b 279 GLN
b 416 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.084868 restraints weight = 21837.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.99
r_work: 0.3029 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6968  Z= 0.171
  Angle     :  0.571   7.842   9465  Z= 0.298
  Chirality :  0.046   0.365   1036
  Planarity :  0.005   0.039   1229
  Dihedral  : 10.128 156.294    981
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 18.14 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.29), residues: 854
  helix:  1.54 (0.27), residues: 384
  sheet:  0.23 (0.41), residues: 145
  loop : -0.49 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG b 241 
 TYR   0.011   0.001   TYR b  59 
 PHE   0.018   0.002   PHE a 255 
 TRP   0.013   0.002   TRP a  21 
 HIS   0.005   0.001   HIS a 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6968)
  covalent geometry    : angle       0.57129 ( 9465)
  hydrogen bonds       : bond        0.06933 (  293)
  hydrogen bonds       : angle       4.20453 (  840)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.392 
Fit side-chains
REVERT: a   50 ASN cc_start: 0.8426 (m110) cc_final: 0.8124 (m-40)
REVERT: a   97 GLU cc_start: 0.7770 (pt0) cc_final: 0.7406 (mt-10)
REVERT: a  279 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7386 (mp0)
REVERT: a  372 GLN cc_start: 0.8727 (mt0) cc_final: 0.8134 (mm110)
REVERT: a  414 GLU cc_start: 0.8071 (mp0) cc_final: 0.7609 (tm-30)
REVERT: b  118 ASP cc_start: 0.7926 (t70) cc_final: 0.7433 (m-30)
REVERT: b  147 MET cc_start: 0.9024 (ttt) cc_final: 0.8595 (ttt)
REVERT: b  164 MET cc_start: 0.8935 (tpp) cc_final: 0.8580 (tpp)
REVERT: b  175 VAL cc_start: 0.8798 (t) cc_final: 0.8351 (p)
REVERT: b  280 GLN cc_start: 0.8153 (mp10) cc_final: 0.7652 (mp10)
REVERT: b  288 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7310 (mm-30)
REVERT: b  336 LYS cc_start: 0.7664 (mptm) cc_final: 0.7265 (mppt)
REVERT: b  338 SER cc_start: 0.7706 (p) cc_final: 0.7501 (t)
REVERT: b  347 ASN cc_start: 0.7491 (t0) cc_final: 0.7240 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 91
  average time/residue: 1.3367
  time to fit residues: 127.6414
Evaluate side-chains
  88 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   94 THR
Chi-restraints excluded: chain a residue  170 SER
Chi-restraints excluded: chain a residue  193 THR
Chi-restraints excluded: chain a residue  349 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0070
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
b 279 GLN
b 416 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.108928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.088821 restraints weight = 21607.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.02
r_work: 0.3088 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6968  Z= 0.105
  Angle     :  0.499   6.474   9465  Z= 0.260
  Chirality :  0.043   0.359   1036
  Planarity :  0.004   0.038   1229
  Dihedral  :  9.440 149.553    981
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 18.14 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.29), residues: 854
  helix:  1.71 (0.27), residues: 385
  sheet:  0.27 (0.41), residues: 150
  loop : -0.50 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a 105 
 TYR   0.007   0.001   TYR b  59 
 PHE   0.009   0.001   PHE a 255 
 TRP   0.016   0.001   TRP a  21 
 HIS   0.003   0.001   HIS a 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6968)
  covalent geometry    : angle       0.49909 ( 9465)
  hydrogen bonds       : bond        0.05209 (  293)
  hydrogen bonds       : angle       3.97741 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5223.20 seconds
wall clock time: 88 minutes 58.70 seconds (5338.70 seconds total)