Starting phenix.real_space_refine
on Tue Mar  3 20:33:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jvp_22509/03_2026/7jvp_22509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jvp_22509/03_2026/7jvp_22509.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jvp_22509/03_2026/7jvp_22509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jvp_22509/03_2026/7jvp_22509.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jvp_22509/03_2026/7jvp_22509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jvp_22509/03_2026/7jvp_22509.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     Cl      1      4.86       5
     C    5462      2.51       5
     N    1440      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8486
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2227
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1966
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2604
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 280
          Unusual residues: {'CLR': 6, 'PLM': 5, 'SK9': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 2.21, per 1000 atoms: 0.26
  Number of scatterers: 8486
  At special positions: 0
  Unit cell: (97.185, 106.59, 122.265, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      53     16.00
     O    1530      8.00
     N    1440      7.00
     C    5462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 614.8 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      45.7% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 51 through 57
      removed outlier: 3.519A  pdb=" N   ARG R  55 " --> pdb=" O   PHE R  51 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS R  57 " --> pdb=" O   HIS R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 77
      removed outlier: 4.392A  pdb=" N   PHE R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
      removed outlier: 3.661A  pdb=" N   LYS R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 127
      removed outlier: 4.380A  pdb=" N   ILE R  98 " --> pdb=" O   SER R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 161
      removed outlier: 4.141A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 191 through 203
    Processing helix  chain 'R' and resid 203 through 239
    Processing helix  chain 'R' and resid 265 through 299
      Proline residue:  R 287  - end of helix
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 309 through 332
      removed outlier: 3.598A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 346
    Processing helix  chain 'A' and resid 10 through 40
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.877A  pdb=" N   GLN A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 4.244A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 280 through 284
      removed outlier: 3.671A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 284'
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 312 through 317
      removed outlier: 4.033A  pdb=" N   ALA A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 317'
    Processing helix  chain 'A' and resid 331 through 353
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.504A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.848A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 3.924A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.744A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.880A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.182A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 5.836A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.704A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.864A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.855A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.051A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1347 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2656
        1.34 -     1.46: 1951
        1.46 -     1.58: 3987
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 8667
  Sorted by residual:
  bond pdb=" N   LEU R 291 "
       pdb=" CA  LEU R 291 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.23e-02 6.61e+03 5.36e+00
  bond pdb=" N   PHE R 313 "
       pdb=" CA  PHE R 313 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.19e-02 7.06e+03 4.74e+00
  bond pdb=" C05 SK9 R 501 "
       pdb=" C07 SK9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C   ILE R 205 "
       pdb=" N   PRO R 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.028 1.36e-02 5.41e+03 4.11e+00
  bond pdb=" C18 SK9 R 501 "
       pdb=" N01 SK9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.448  1.409  0.039 2.00e-02 2.50e+03 3.83e+00
  ... (remaining 8662 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 11122
        2.01 -     4.01: 535
        4.01 -     6.02: 63
        6.02 -     8.03: 18
        8.03 -    10.03: 3
  Bond angle restraints: 11741
  Sorted by residual:
  angle pdb=" C   CYS A 365 "
        pdb=" N   SER A 366 "
        pdb=" CA  SER A 366 "
      ideal   model   delta    sigma   weight residual
     121.54  130.19   -8.65 1.91e+00 2.74e-01 2.05e+01
  angle pdb=" N   LEU R 295 "
        pdb=" CA  LEU R 295 "
        pdb=" C   LEU R 295 "
      ideal   model   delta    sigma   weight residual
     113.16  118.65   -5.49 1.42e+00 4.96e-01 1.49e+01
  angle pdb=" C   CYS B 250 "
        pdb=" N   ARG B 251 "
        pdb=" CA  ARG B 251 "
      ideal   model   delta    sigma   weight residual
     122.99  117.69    5.30 1.41e+00 5.03e-01 1.41e+01
  angle pdb=" C   CYS B 166 "
        pdb=" N   ALA B 167 "
        pdb=" CA  ALA B 167 "
      ideal   model   delta    sigma   weight residual
     122.62  117.27    5.35 1.56e+00 4.11e-01 1.18e+01
  angle pdb=" C07 SK9 R 501 "
        pdb=" C09 SK9 R 501 "
        pdb=" N01 SK9 R 501 "
      ideal   model   delta    sigma   weight residual
     114.07  124.10  -10.03 3.00e+00 1.11e-01 1.12e+01
  ... (remaining 11736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 5207
       15.07 -    30.14: 224
       30.14 -    45.22: 35
       45.22 -    60.29: 9
       60.29 -    75.36: 2
  Dihedral angle restraints: 5477
    sinusoidal: 2448
      harmonic: 3029
  Sorted by residual:
  dihedral pdb=" CA  ASP B 291 "
           pdb=" C   ASP B 291 "
           pdb=" N   PHE B 292 "
           pdb=" CA  PHE B 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.18   21.82     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  TYR N  60 "
           pdb=" C   TYR N  60 "
           pdb=" N   THR N  61 "
           pdb=" CA  THR N  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.84   18.16     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CB  CYS R 298 "
           pdb=" SG  CYS R 298 "
           pdb=" SG  CYS R 307 "
           pdb=" CB  CYS R 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -115.08   29.08     1      1.00e+01 1.00e-02 1.21e+01
  ... (remaining 5474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1133
       0.087 -    0.174: 163
       0.174 -    0.261: 22
       0.261 -    0.348: 6
       0.348 -    0.435: 6
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" C14 CLR R 507 "
            pdb=" C13 CLR R 507 "
            pdb=" C15 CLR R 507 "
            pdb=" C8  CLR R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.75    0.44 2.00e-01 2.50e+01 4.74e+00
  chirality pdb=" C14 CLR R 504 "
            pdb=" C13 CLR R 504 "
            pdb=" C15 CLR R 504 "
            pdb=" C8  CLR R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" C14 CLR R 503 "
            pdb=" C13 CLR R 503 "
            pdb=" C15 CLR R 503 "
            pdb=" C8  CLR R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.40 2.00e-01 2.50e+01 4.09e+00
  ... (remaining 1327 not shown)

  Planarity restraints: 1447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 380 "    0.018 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   ARG A 380 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   ARG A 380 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ASP A 381 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 375 "   -0.016 2.00e-02 2.50e+03   3.12e-02 9.72e+00
        pdb=" C   VAL A 375 "    0.054 2.00e-02 2.50e+03
        pdb=" O   VAL A 375 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE A 376 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 360 "   -0.049 5.00e-02 4.00e+02   7.52e-02 9.05e+00
        pdb=" N   PRO A 361 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1444 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 474
        2.75 -     3.28: 8315
        3.28 -     3.82: 14214
        3.82 -     4.36: 16907
        4.36 -     4.90: 29451
  Nonbonded interactions: 69361
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER R 198 "
            pdb=" OG  SER R 202 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.268 3.040
  ... (remaining 69356 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:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.190
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
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      :  0.005   0.059   8670  Z= 0.260
  Angle     :  0.966  10.032  11747  Z= 0.535
  Chirality :  0.070   0.435   1330
  Planarity :  0.007   0.075   1447
  Dihedral  :  9.005  75.358   3500
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.24), residues: 1021
  helix:  3.52 (0.21), residues: 423
  sheet:  2.92 (0.34), residues: 196
  loop : -1.16 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG R 266 
 TYR   0.023   0.003   TYR A 311 
 PHE   0.041   0.004   PHE B 234 
 TRP   0.030   0.004   TRP A 281 
 HIS   0.019   0.004   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 8667)
  covalent geometry    : angle       0.96507 (11741)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       1.97513 (    6)
  hydrogen bonds       : bond        0.13726 (  462)
  hydrogen bonds       : angle       6.22628 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  278 MET cc_start: 0.7523 (mmm) cc_final: 0.7252 (mmp)
REVERT: A   17 LYS cc_start: 0.7640 (tttt) cc_final: 0.7074 (mmmt)
REVERT: A  378 ASP cc_start: 0.7661 (m-30) cc_final: 0.7416 (m-30)
REVERT: B  161 SER cc_start: 0.8590 (t) cc_final: 0.8082 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.5765
  time to fit residues: 151.0302
Evaluate side-chains
  149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 311 ASN
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
A 294 GLN
B   6 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
B 110 ASN
B 156 GLN
B 259 GLN
N  31 ASN
N  39 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.163152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.130384 restraints weight = 9862.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.85
r_work: 0.3349 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8670  Z= 0.160
  Angle     :  0.554   7.536  11747  Z= 0.299
  Chirality :  0.043   0.147   1330
  Planarity :  0.005   0.047   1447
  Dihedral  :  6.557  57.855   1608
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.87 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.25), residues: 1021
  helix:  3.18 (0.23), residues: 429
  sheet:  1.82 (0.33), residues: 210
  loop : -0.63 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 356 
 TYR   0.016   0.002   TYR A 339 
 PHE   0.016   0.002   PHE R 288 
 TRP   0.026   0.002   TRP A 281 
 HIS   0.010   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8667)
  covalent geometry    : angle       0.55337 (11741)
  SS BOND              : bond        0.01051 (    3)
  SS BOND              : angle       1.06477 (    6)
  hydrogen bonds       : bond        0.04908 (  462)
  hydrogen bonds       : angle       4.79579 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.316 
Fit side-chains
REVERT: R   59 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8663 (p)
REVERT: R  213 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8517 (m)
REVERT: R  216 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7769 (mtt180)
REVERT: R  219 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7455 (mtt-85)
REVERT: R  278 MET cc_start: 0.8122 (mmm) cc_final: 0.7834 (mmp)
REVERT: A   17 LYS cc_start: 0.7363 (tttt) cc_final: 0.6589 (mmmt)
REVERT: A  209 GLU cc_start: 0.7525 (tt0) cc_final: 0.7309 (tp30)
REVERT: A  344 GLU cc_start: 0.7888 (tp30) cc_final: 0.7655 (tp30)
REVERT: A  378 ASP cc_start: 0.8343 (m-30) cc_final: 0.8138 (m-30)
REVERT: A  386 MET cc_start: 0.8880 (ttm) cc_final: 0.8588 (ttp)
REVERT: B   96 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7856 (mtp85)
REVERT: B  266 HIS cc_start: 0.7804 (t-170) cc_final: 0.7549 (t-170)
REVERT: N    5 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7125 (tm-30)
REVERT: N   46 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8131 (pm20)
  outliers start: 24
  outliers final: 6
  residues processed: 203
  average time/residue: 0.6139
  time to fit residues: 132.2221
Evaluate side-chains
  158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  324 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   46 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.160741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.127854 restraints weight = 9595.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.87
r_work: 0.3236 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8670  Z= 0.149
  Angle     :  0.522   7.792  11747  Z= 0.280
  Chirality :  0.041   0.138   1330
  Planarity :  0.004   0.039   1447
  Dihedral  :  6.373  58.434   1608
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.68 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.25), residues: 1021
  helix:  2.97 (0.23), residues: 423
  sheet:  1.12 (0.32), residues: 209
  loop : -0.32 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 228 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.025   0.002   PHE R 297 
 TRP   0.017   0.002   TRP A 281 
 HIS   0.008   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8667)
  covalent geometry    : angle       0.52094 (11741)
  SS BOND              : bond        0.00484 (    3)
  SS BOND              : angle       1.82675 (    6)
  hydrogen bonds       : bond        0.04548 (  462)
  hydrogen bonds       : angle       4.66402 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.330 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6741 (mmt90) cc_final: 0.5738 (tpp-160)
REVERT: R  213 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8695 (m)
REVERT: R  219 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7446 (mtt-85)
REVERT: R  278 MET cc_start: 0.8279 (mmm) cc_final: 0.8025 (mmp)
REVERT: A   17 LYS cc_start: 0.7322 (tttt) cc_final: 0.6538 (mmmt)
REVERT: A  265 ARG cc_start: 0.7766 (ptt180) cc_final: 0.7408 (ppt-90)
REVERT: A  307 LYS cc_start: 0.4921 (mmtt) cc_final: 0.4697 (mtpm)
REVERT: A  330 GLU cc_start: 0.5929 (tt0) cc_final: 0.5130 (tp30)
REVERT: A  370 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6988 (pt0)
REVERT: A  386 MET cc_start: 0.8909 (ttm) cc_final: 0.8603 (ttp)
REVERT: A  392 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7519 (tt0)
REVERT: B   42 ARG cc_start: 0.6920 (tpt170) cc_final: 0.6698 (tpt170)
REVERT: B   96 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7907 (mtp85)
REVERT: B  262 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8310 (ttm)
REVERT: G   46 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7469 (mppt)
REVERT: N    5 GLN cc_start: 0.7919 (mm-40) cc_final: 0.6952 (tm-30)
REVERT: N   38 ARG cc_start: 0.8700 (ptt-90) cc_final: 0.8300 (ptp90)
REVERT: N   46 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8206 (pm20)
  outliers start: 28
  outliers final: 15
  residues processed: 167
  average time/residue: 0.6400
  time to fit residues: 113.1853
Evaluate side-chains
  159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  324 SER
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 7 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
N  31 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.153795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.118724 restraints weight = 9764.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.00
r_work: 0.3234 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8670  Z= 0.141
  Angle     :  0.504   7.874  11747  Z= 0.268
  Chirality :  0.040   0.135   1330
  Planarity :  0.004   0.040   1447
  Dihedral  :  6.005  55.421   1608
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 15.23 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.26), residues: 1021
  helix:  2.84 (0.24), residues: 422
  sheet:  0.61 (0.31), residues: 215
  loop : -0.21 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 356 
 TYR   0.012   0.001   TYR R 194 
 PHE   0.017   0.001   PHE R 288 
 TRP   0.015   0.002   TRP A 281 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8667)
  covalent geometry    : angle       0.50368 (11741)
  SS BOND              : bond        0.00283 (    3)
  SS BOND              : angle       0.99745 (    6)
  hydrogen bonds       : bond        0.04342 (  462)
  hydrogen bonds       : angle       4.66436 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 153
  time to evaluate  : 0.316 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6843 (mmt90) cc_final: 0.5858 (tpp-160)
REVERT: R  213 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8768 (m)
REVERT: R  219 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7514 (mtt-85)
REVERT: A   16 GLU cc_start: 0.6917 (tp30) cc_final: 0.6684 (tp30)
REVERT: A   17 LYS cc_start: 0.7325 (tttt) cc_final: 0.6603 (mmmt)
REVERT: A   20 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7269 (mtm-85)
REVERT: A  265 ARG cc_start: 0.7814 (ptt180) cc_final: 0.7507 (ppt-90)
REVERT: A  330 GLU cc_start: 0.5934 (tt0) cc_final: 0.5290 (tp30)
REVERT: A  378 ASP cc_start: 0.8557 (m-30) cc_final: 0.8099 (m-30)
REVERT: A  386 MET cc_start: 0.8934 (ttm) cc_final: 0.8646 (ttp)
REVERT: B   96 ARG cc_start: 0.8269 (mtt180) cc_final: 0.8006 (mtp85)
REVERT: G   46 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7448 (mppt)
REVERT: N    3 GLN cc_start: 0.8174 (pt0) cc_final: 0.7313 (tp-100)
REVERT: N    5 GLN cc_start: 0.8082 (mm-40) cc_final: 0.6942 (tm-30)
REVERT: N   38 ARG cc_start: 0.8692 (ptt-90) cc_final: 0.8340 (ptp90)
REVERT: N   46 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8234 (pm20)
  outliers start: 39
  outliers final: 17
  residues processed: 174
  average time/residue: 0.6524
  time to fit residues: 119.9173
Evaluate side-chains
  159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0980
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 92 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.153349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.118570 restraints weight = 9775.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.99
r_work: 0.3194 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8670  Z= 0.127
  Angle     :  0.493   6.520  11747  Z= 0.263
  Chirality :  0.040   0.136   1330
  Planarity :  0.004   0.039   1447
  Dihedral  :  5.908  56.614   1608
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 16.24 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.26), residues: 1021
  helix:  2.84 (0.24), residues: 418
  sheet:  0.44 (0.32), residues: 205
  loop : -0.26 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 356 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.018   0.001   PHE R 288 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8667)
  covalent geometry    : angle       0.49266 (11741)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       0.74080 (    6)
  hydrogen bonds       : bond        0.04192 (  462)
  hydrogen bonds       : angle       4.60773 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 0.328 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6783 (mmt90) cc_final: 0.5794 (tpp-160)
REVERT: R  213 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8379 (p)
REVERT: R  219 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7517 (mtt-85)
REVERT: A   17 LYS cc_start: 0.7300 (tttt) cc_final: 0.6590 (mmmt)
REVERT: A  265 ARG cc_start: 0.7813 (ptt180) cc_final: 0.7536 (ppt-90)
REVERT: A  307 LYS cc_start: 0.4629 (OUTLIER) cc_final: 0.4287 (mtmm)
REVERT: A  378 ASP cc_start: 0.8535 (m-30) cc_final: 0.8080 (m-30)
REVERT: A  386 MET cc_start: 0.8971 (ttm) cc_final: 0.8674 (ttp)
REVERT: A  392 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7647 (tt0)
REVERT: G   46 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7491 (mppt)
REVERT: N    3 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7308 (tp-100)
REVERT: N    5 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7063 (tm-30)
REVERT: N   38 ARG cc_start: 0.8674 (ptt-90) cc_final: 0.8400 (ptp90)
REVERT: N   46 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8305 (pm20)
  outliers start: 43
  outliers final: 20
  residues processed: 173
  average time/residue: 0.6459
  time to fit residues: 118.1967
Evaluate side-chains
  159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
N  31 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.152218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.117588 restraints weight = 9690.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.98
r_work: 0.3178 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8670  Z= 0.139
  Angle     :  0.500   6.194  11747  Z= 0.266
  Chirality :  0.040   0.137   1330
  Planarity :  0.004   0.041   1447
  Dihedral  :  5.934  55.953   1608
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 17.02 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.26), residues: 1021
  helix:  2.75 (0.24), residues: 419
  sheet:  0.21 (0.32), residues: 214
  loop : -0.26 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 356 
 TYR   0.014   0.001   TYR N  95 
 PHE   0.018   0.001   PHE R 288 
 TRP   0.012   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8667)
  covalent geometry    : angle       0.49949 (11741)
  SS BOND              : bond        0.00106 (    3)
  SS BOND              : angle       0.84558 (    6)
  hydrogen bonds       : bond        0.04221 (  462)
  hydrogen bonds       : angle       4.66897 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 150
  time to evaluate  : 0.313 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6763 (mmt90) cc_final: 0.5760 (tpp-160)
REVERT: R  213 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8427 (p)
REVERT: R  219 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7540 (mtt-85)
REVERT: R  223 LYS cc_start: 0.8078 (mttt) cc_final: 0.7866 (mtpt)
REVERT: R  265 LYS cc_start: 0.7546 (tttt) cc_final: 0.7237 (tmtm)
REVERT: R  278 MET cc_start: 0.8650 (mmm) cc_final: 0.8448 (mmm)
REVERT: A   17 LYS cc_start: 0.7355 (tttt) cc_final: 0.6608 (mmmt)
REVERT: A  265 ARG cc_start: 0.7834 (ptt180) cc_final: 0.7608 (ppt-90)
REVERT: A  307 LYS cc_start: 0.4495 (mtpm) cc_final: 0.4150 (mtmm)
REVERT: A  314 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7817 (pm20)
REVERT: A  370 GLU cc_start: 0.7486 (pm20) cc_final: 0.6794 (mm-30)
REVERT: A  378 ASP cc_start: 0.8562 (m-30) cc_final: 0.8078 (m-30)
REVERT: A  386 MET cc_start: 0.8968 (ttm) cc_final: 0.8677 (ttp)
REVERT: A  392 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7611 (tt0)
REVERT: G   46 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7549 (mppt)
REVERT: N    3 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7670 (tt0)
REVERT: N    5 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7079 (tm-30)
REVERT: N   38 ARG cc_start: 0.8687 (ptt-90) cc_final: 0.8454 (ptp90)
REVERT: N   46 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8282 (pm20)
REVERT: N  110 VAL cc_start: 0.9057 (t) cc_final: 0.8764 (m)
  outliers start: 37
  outliers final: 20
  residues processed: 173
  average time/residue: 0.7089
  time to fit residues: 128.9966
Evaluate side-chains
  161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.150486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.115470 restraints weight = 9885.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.99
r_work: 0.3155 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8670  Z= 0.146
  Angle     :  0.512   6.417  11747  Z= 0.272
  Chirality :  0.040   0.136   1330
  Planarity :  0.004   0.042   1447
  Dihedral  :  5.975  56.155   1608
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 18.25 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.58 (0.26), residues: 1021
  helix:  2.62 (0.24), residues: 431
  sheet:  0.05 (0.31), residues: 221
  loop : -0.16 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 356 
 TYR   0.017   0.001   TYR N  95 
 PHE   0.019   0.001   PHE R 288 
 TRP   0.012   0.002   TRP R  99 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8667)
  covalent geometry    : angle       0.51170 (11741)
  SS BOND              : bond        0.00085 (    3)
  SS BOND              : angle       1.02503 (    6)
  hydrogen bonds       : bond        0.04235 (  462)
  hydrogen bonds       : angle       4.69845 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 0.318 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6641 (mmt90) cc_final: 0.5819 (tpm170)
REVERT: R   57 LYS cc_start: 0.7228 (mttt) cc_final: 0.6875 (mtmm)
REVERT: R  213 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8425 (p)
REVERT: R  219 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7540 (mtt-85)
REVERT: R  223 LYS cc_start: 0.8077 (mttt) cc_final: 0.7863 (mtpt)
REVERT: R  265 LYS cc_start: 0.7559 (tttt) cc_final: 0.7245 (tmtm)
REVERT: A   17 LYS cc_start: 0.7362 (tttt) cc_final: 0.6611 (mmmt)
REVERT: A  307 LYS cc_start: 0.4539 (OUTLIER) cc_final: 0.4237 (mtmm)
REVERT: A  314 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7883 (pm20)
REVERT: A  344 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8158 (mm-30)
REVERT: A  356 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7562 (tpp80)
REVERT: A  370 GLU cc_start: 0.7548 (pm20) cc_final: 0.7251 (pm20)
REVERT: A  378 ASP cc_start: 0.8562 (m-30) cc_final: 0.8077 (m-30)
REVERT: A  386 MET cc_start: 0.8953 (ttm) cc_final: 0.8664 (ttp)
REVERT: B  146 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8675 (mp)
REVERT: G   46 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7542 (mppt)
REVERT: N    3 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7678 (tt0)
REVERT: N    5 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7219 (tm-30)
REVERT: N   38 ARG cc_start: 0.8735 (ptt-90) cc_final: 0.8496 (ptp90)
REVERT: N   46 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8286 (pm20)
REVERT: N  110 VAL cc_start: 0.9031 (t) cc_final: 0.8739 (m)
  outliers start: 37
  outliers final: 23
  residues processed: 166
  average time/residue: 0.5970
  time to fit residues: 104.9641
Evaluate side-chains
  162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0870
   chunk 21 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
B 259 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.151642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.117038 restraints weight = 9789.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.97
r_work: 0.3165 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8670  Z= 0.128
  Angle     :  0.495   5.922  11747  Z= 0.264
  Chirality :  0.039   0.134   1330
  Planarity :  0.004   0.037   1447
  Dihedral  :  5.888  59.581   1608
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.37 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.26), residues: 1021
  helix:  2.62 (0.24), residues: 432
  sheet:  0.06 (0.32), residues: 210
  loop : -0.13 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 356 
 TYR   0.015   0.001   TYR N  95 
 PHE   0.018   0.001   PHE R 288 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8667)
  covalent geometry    : angle       0.49468 (11741)
  SS BOND              : bond        0.00077 (    3)
  SS BOND              : angle       0.92323 (    6)
  hydrogen bonds       : bond        0.04119 (  462)
  hydrogen bonds       : angle       4.64751 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.301 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6626 (mmt90) cc_final: 0.5832 (tpm170)
REVERT: R   57 LYS cc_start: 0.7321 (mttt) cc_final: 0.6967 (mtmm)
REVERT: R  134 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8065 (mmmm)
REVERT: R  213 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8403 (p)
REVERT: R  219 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7538 (mtt-85)
REVERT: R  223 LYS cc_start: 0.8084 (mttt) cc_final: 0.7864 (mtpt)
REVERT: R  265 LYS cc_start: 0.7567 (tttt) cc_final: 0.7256 (tmtm)
REVERT: R  269 LYS cc_start: 0.8095 (tttt) cc_final: 0.7568 (ptmm)
REVERT: R  278 MET cc_start: 0.8657 (mmm) cc_final: 0.8447 (mmm)
REVERT: A   17 LYS cc_start: 0.7456 (tttt) cc_final: 0.6623 (mmmt)
REVERT: A  307 LYS cc_start: 0.4481 (OUTLIER) cc_final: 0.4169 (mtmm)
REVERT: A  314 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8007 (pm20)
REVERT: A  344 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8111 (mm-30)
REVERT: A  356 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7560 (tpp80)
REVERT: A  370 GLU cc_start: 0.7576 (pm20) cc_final: 0.7266 (pm20)
REVERT: A  378 ASP cc_start: 0.8553 (m-30) cc_final: 0.8103 (m-30)
REVERT: A  386 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8687 (ttp)
REVERT: B  146 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8629 (mp)
REVERT: N    3 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7713 (tt0)
REVERT: N    5 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7176 (tm-30)
REVERT: N   38 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.8207 (ptp90)
REVERT: N   46 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8279 (pm20)
REVERT: N   87 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7930 (mtmt)
REVERT: N  110 VAL cc_start: 0.9021 (t) cc_final: 0.8769 (m)
  outliers start: 33
  outliers final: 19
  residues processed: 163
  average time/residue: 0.6497
  time to fit residues: 111.8976
Evaluate side-chains
  158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0870
   chunk 46 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
R 164 HIS
A 377 ASN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.152750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.118800 restraints weight = 9815.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.91
r_work: 0.3193 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8670  Z= 0.125
  Angle     :  0.499   6.688  11747  Z= 0.265
  Chirality :  0.040   0.150   1330
  Planarity :  0.004   0.037   1447
  Dihedral  :  5.828  58.990   1608
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.38 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.60 (0.26), residues: 1021
  helix:  2.64 (0.24), residues: 432
  sheet: -0.00 (0.31), residues: 220
  loop : -0.13 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 356 
 TYR   0.012   0.001   TYR N  95 
 PHE   0.018   0.001   PHE R 288 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8667)
  covalent geometry    : angle       0.49918 (11741)
  SS BOND              : bond        0.00064 (    3)
  SS BOND              : angle       0.85196 (    6)
  hydrogen bonds       : bond        0.04075 (  462)
  hydrogen bonds       : angle       4.63876 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.310 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6641 (mmt90) cc_final: 0.5784 (tpm170)
REVERT: R   57 LYS cc_start: 0.7362 (mttt) cc_final: 0.6993 (mtmm)
REVERT: R  134 LYS cc_start: 0.8234 (mmmt) cc_final: 0.8019 (mmmm)
REVERT: R  213 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8378 (p)
REVERT: R  219 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7467 (mtt-85)
REVERT: R  223 LYS cc_start: 0.8025 (mttt) cc_final: 0.7819 (mtpt)
REVERT: R  265 LYS cc_start: 0.7547 (tttt) cc_final: 0.7217 (tmtm)
REVERT: A   17 LYS cc_start: 0.7421 (tttt) cc_final: 0.6580 (mmmt)
REVERT: A  307 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.4289 (mtmm)
REVERT: A  314 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7994 (pm20)
REVERT: A  344 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: A  356 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7530 (tpp80)
REVERT: A  386 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8659 (ttp)
REVERT: B  124 TYR cc_start: 0.8931 (m-80) cc_final: 0.8555 (m-80)
REVERT: B  146 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8596 (mp)
REVERT: N    3 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7682 (tt0)
REVERT: N    5 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7171 (tm-30)
REVERT: N   38 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8174 (ptp90)
REVERT: N   46 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8276 (pm20)
REVERT: N   87 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7906 (mtmt)
REVERT: N  110 VAL cc_start: 0.8988 (t) cc_final: 0.8740 (m)
  outliers start: 30
  outliers final: 19
  residues processed: 152
  average time/residue: 0.6625
  time to fit residues: 106.3595
Evaluate side-chains
  161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0470
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7678

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.151925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.117881 restraints weight = 9717.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.89
r_work: 0.3186 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8670  Z= 0.139
  Angle     :  0.510   7.041  11747  Z= 0.272
  Chirality :  0.040   0.134   1330
  Planarity :  0.004   0.043   1447
  Dihedral  :  5.898  58.287   1608
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.83 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.26), residues: 1021
  helix:  2.57 (0.24), residues: 433
  sheet: -0.08 (0.31), residues: 222
  loop : -0.10 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 226 
 TYR   0.011   0.001   TYR R 194 
 PHE   0.018   0.001   PHE R 288 
 TRP   0.012   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8667)
  covalent geometry    : angle       0.51008 (11741)
  SS BOND              : bond        0.00047 (    3)
  SS BOND              : angle       0.98851 (    6)
  hydrogen bonds       : bond        0.04146 (  462)
  hydrogen bonds       : angle       4.68436 ( 1347)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.296 
Fit side-chains
REVERT: R   50 ARG cc_start: 0.6675 (mmt90) cc_final: 0.5803 (tpm170)
REVERT: R   57 LYS cc_start: 0.7375 (mttt) cc_final: 0.6997 (mtmm)
REVERT: R  213 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8400 (p)
REVERT: R  219 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7459 (mtt-85)
REVERT: R  223 LYS cc_start: 0.8004 (mttt) cc_final: 0.7786 (mtpt)
REVERT: R  265 LYS cc_start: 0.7533 (tttt) cc_final: 0.7216 (tmtm)
REVERT: R  269 LYS cc_start: 0.8074 (tttt) cc_final: 0.7509 (ptmm)
REVERT: R  278 MET cc_start: 0.8636 (mmm) cc_final: 0.8410 (mmm)
REVERT: A   17 LYS cc_start: 0.7404 (tttt) cc_final: 0.6570 (mmmt)
REVERT: A  307 LYS cc_start: 0.4666 (OUTLIER) cc_final: 0.4364 (mtmm)
REVERT: A  314 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8044 (pm20)
REVERT: A  344 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: A  378 ASP cc_start: 0.8580 (m-30) cc_final: 0.8134 (m-30)
REVERT: A  386 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8615 (ttp)
REVERT: B  146 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8635 (mp)
REVERT: N    3 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7683 (tt0)
REVERT: N    5 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7168 (tm-30)
REVERT: N   38 ARG cc_start: 0.8723 (ptt-90) cc_final: 0.8194 (ptp90)
REVERT: N   46 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8243 (pm20)
REVERT: N   87 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7934 (mtmt)
REVERT: N  110 VAL cc_start: 0.8996 (t) cc_final: 0.8737 (m)
  outliers start: 31
  outliers final: 22
  residues processed: 159
  average time/residue: 0.6925
  time to fit residues: 116.0209
Evaluate side-chains
  161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  197 SER
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 52 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.151581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117254 restraints weight = 9717.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.90
r_work: 0.3148 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8670  Z= 0.149
  Angle     :  0.531   8.803  11747  Z= 0.279
  Chirality :  0.040   0.134   1330
  Planarity :  0.004   0.055   1447
  Dihedral  :  6.020  57.837   1608
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.05 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.26), residues: 1021
  helix:  2.52 (0.24), residues: 432
  sheet: -0.13 (0.31), residues: 221
  loop : -0.13 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  19 
 TYR   0.012   0.001   TYR R 194 
 PHE   0.019   0.001   PHE R 288 
 TRP   0.012   0.002   TRP R  80 
 HIS   0.006   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8667)
  covalent geometry    : angle       0.53069 (11741)
  SS BOND              : bond        0.00079 (    3)
  SS BOND              : angle       1.11243 (    6)
  hydrogen bonds       : bond        0.04200 (  462)
  hydrogen bonds       : angle       4.75133 ( 1347)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3485.82 seconds
wall clock time: 60 minutes 6.00 seconds (3606.00 seconds total)