Starting phenix.real_space_refine
on Sat Aug 23 02:42:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byo_45040/08_2025/9byo_45040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byo_45040/08_2025/9byo_45040.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byo_45040/08_2025/9byo_45040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byo_45040/08_2025/9byo_45040.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byo_45040/08_2025/9byo_45040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byo_45040/08_2025/9byo_45040.map"
  }
  resolution = 2.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5956      2.51       5
     N    1625      2.21       5
     O    1743      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9380
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "R"
      Number of atoms: 3179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3179
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 14, 'TRANS': 369}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 238
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "A"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1959
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "P"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.42, per 1000 atoms: 0.26
  Number of scatterers: 9380
  At special positions: 0
  Unit cell: (78.85, 97.11, 175.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1743      8.00
     N    1625      7.00
     C    5956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 0.89
  Conformation dependent library (CDL) restraints added in 256.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 12 sheets defined
      45.0% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 53
      removed outlier: 3.546A  pdb=" N   GLN R  45 " --> pdb=" O   GLU R  41 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   THR R  51 " --> pdb=" O   GLN R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 169
    Processing helix  chain 'R' and resid 170 through 173
    Processing helix  chain 'R' and resid 174 through 205
    Processing helix  chain 'R' and resid 206 through 216
    Processing helix  chain 'R' and resid 219 through 222
    Processing helix  chain 'R' and resid 223 through 256
      removed outlier: 3.935A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   PHE R 230 " --> pdb=" O   CYS R 226 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 276
    Processing helix  chain 'R' and resid 277 through 292
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 302 through 338
      removed outlier: 3.727A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 364 through 369
      removed outlier: 4.535A  pdb=" N   PHE R 369 " --> pdb=" O   VAL R 365 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 371 through 376
      removed outlier: 6.155A  pdb=" N   ARG R 376 " --> pdb=" O   GLU R 373 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 377 through 403
      removed outlier: 4.019A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 422
    Processing helix  chain 'P' and resid 2 through 28
      removed outlier: 3.676A  pdb=" N   ASN P  28 " --> pdb=" O   GLU P  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.522A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.551A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.741A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.521A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.095A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.752A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.506A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66
    Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 84
      removed outlier: 3.629A  pdb=" N   CYS R 104 " --> pdb=" O   SER R  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.323A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.216A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.404A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.694A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.767A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.628A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.512A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.491A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.713A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.155A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    504 hydrogen bonds defined for protein.
    1425 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: 1.71

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1945
        1.33 -     1.45: 2378
        1.45 -     1.57: 5179
        1.57 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 9578
  Sorted by residual:
  bond pdb=" C   LEU P  10 "
       pdb=" N   SER P  11 "
    ideal  model  delta    sigma   weight residual
    1.335  1.283  0.052 1.36e-02 5.41e+03 1.46e+01
  bond pdb=" C   HIS R 212 "
       pdb=" N   GLN R 213 "
    ideal  model  delta    sigma   weight residual
    1.335  1.284  0.052 1.38e-02 5.25e+03 1.39e+01
  bond pdb=" C   TRP P  25 "
       pdb=" N   LEU P  26 "
    ideal  model  delta    sigma   weight residual
    1.334  1.288  0.047 1.27e-02 6.20e+03 1.36e+01
  bond pdb=" C   SER P  11 "
       pdb=" N   LYS P  12 "
    ideal  model  delta    sigma   weight residual
    1.335  1.380 -0.045 1.31e-02 5.83e+03 1.16e+01
  bond pdb=" CA  SER R 206 "
       pdb=" CB  SER R 206 "
    ideal  model  delta    sigma   weight residual
    1.528  1.474  0.054 1.61e-02 3.86e+03 1.10e+01
  ... (remaining 9573 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 12451
        1.99 -     3.97: 467
        3.97 -     5.96: 48
        5.96 -     7.95: 7
        7.95 -     9.93: 3
  Bond angle restraints: 12976
  Sorted by residual:
  angle pdb=" N   PHE R 143 "
        pdb=" CA  PHE R 143 "
        pdb=" C   PHE R 143 "
      ideal   model   delta    sigma   weight residual
     111.28  105.11    6.17 1.09e+00 8.42e-01 3.20e+01
  angle pdb=" N   ALA R 256 "
        pdb=" CA  ALA R 256 "
        pdb=" C   ALA R 256 "
      ideal   model   delta    sigma   weight residual
     113.01  106.38    6.63 1.20e+00 6.94e-01 3.05e+01
  angle pdb=" CA  PHE R 413 "
        pdb=" CB  PHE R 413 "
        pdb=" CG  PHE R 413 "
      ideal   model   delta    sigma   weight residual
     113.80  119.32   -5.52 1.00e+00 1.00e+00 3.05e+01
  angle pdb=" C   PHE R 369 "
        pdb=" CA  PHE R 369 "
        pdb=" CB  PHE R 369 "
      ideal   model   delta    sigma   weight residual
     110.01  119.94   -9.93 1.80e+00 3.09e-01 3.05e+01
  angle pdb=" N   SER A  51 "
        pdb=" CA  SER A  51 "
        pdb=" C   SER A  51 "
      ideal   model   delta    sigma   weight residual
     114.31  107.59    6.72 1.29e+00 6.01e-01 2.71e+01
  ... (remaining 12971 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5280
       17.99 -    35.98: 307
       35.98 -    53.97: 60
       53.97 -    71.96: 13
       71.96 -    89.95: 13
  Dihedral angle restraints: 5673
    sinusoidal: 2267
      harmonic: 3406
  Sorted by residual:
  dihedral pdb=" CB  CYS R  62 "
           pdb=" SG  CYS R  62 "
           pdb=" SG  CYS R 104 "
           pdb=" CB  CYS R 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -32.45  -53.55     1      1.00e+01 1.00e-02 3.90e+01
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.36  -23.64     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.16   21.84     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 5670 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1178
       0.065 -    0.130: 211
       0.130 -    0.195: 23
       0.195 -    0.260: 8
       0.260 -    0.325: 4
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CA  VAL R 370 "
            pdb=" N   VAL R 370 "
            pdb=" C   VAL R 370 "
            pdb=" CB  VAL R 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.77   -0.33 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CA  PHE R 143 "
            pdb=" N   PHE R 143 "
            pdb=" C   PHE R 143 "
            pdb=" CB  PHE R 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  ARG R 326 "
            pdb=" N   ARG R 326 "
            pdb=" C   ARG R 326 "
            pdb=" CB  ARG R 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 1421 not shown)

  Planarity restraints: 1656
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.034 2.00e-02 2.50e+03   3.10e-02 1.92e+01
        pdb=" CG  TYR B  59 "   -0.077 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "   -0.062 5.00e-02 4.00e+02   9.41e-02 1.42e+01
        pdb=" N   PRO N  88 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU P  24 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   GLU P  24 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLU P  24 "    0.021 2.00e-02 2.50e+03
        pdb=" N   TRP P  25 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1653 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 116
        2.65 -     3.21: 8680
        3.21 -     3.77: 15118
        3.77 -     4.34: 22460
        4.34 -     4.90: 34874
  Nonbonded interactions: 81248
  Sorted by model distance:
  nonbonded pdb=" O   HOH R 511 "
            pdb=" O   HOH P 102 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" NH1 ARG B  96 "
            pdb=" OH  TYR B 124 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OE1 GLU R  41 "
            pdb=" NH2 ARG R  44 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" NH1 ARG B  42 "
            pdb=" O   ILE B  43 "
     model   vdw
     2.255 3.120
  ... (remaining 81243 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.860
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.290
  Find NCS groups from input model:        0.050
  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:5.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
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   0.054   9584  Z= 0.329
  Angle     :  0.811   9.935  12988  Z= 0.535
  Chirality :  0.054   0.325   1424
  Planarity :  0.006   0.094   1656
  Dihedral  : 12.956  89.949   3453
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.24), residues: 1150
  helix:  0.83 (0.23), residues: 469
  sheet:  0.40 (0.34), residues: 227
  loop :  0.08 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  96 
 TYR   0.077   0.003   TYR B  59 
 PHE   0.027   0.002   PHE R 413 
 TRP   0.021   0.002   TRP P  25 
 HIS   0.018   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 9578)
  covalent geometry    : angle       0.81027 (12976)
  SS BOND              : bond        0.00358 (    6)
  SS BOND              : angle       1.40843 (   12)
  hydrogen bonds       : bond        0.22170 (  504)
  hydrogen bonds       : angle       7.44993 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: P   12 LYS cc_start: 0.7373 (mttm) cc_final: 0.7151 (mtpp)
  outliers start: 0
  outliers final: 1
  residues processed: 124
  average time/residue: 0.8489
  time to fit residues: 110.5270
Evaluate side-chains
  107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0020
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
R 177 ASN
R 263 GLN
R 302 ASN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.203239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.151750 restraints weight = 9182.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 1.74
r_work: 0.3608 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9584  Z= 0.132
  Angle     :  0.565   6.626  12988  Z= 0.310
  Chirality :  0.042   0.163   1424
  Planarity :  0.005   0.066   1656
  Dihedral  :  4.706  23.858   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  5.74 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.24), residues: 1150
  helix:  1.90 (0.23), residues: 469
  sheet:  0.41 (0.33), residues: 227
  loop :  0.10 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 134 
 TYR   0.036   0.002   TYR R 148 
 PHE   0.012   0.002   PHE R 413 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9578)
  covalent geometry    : angle       0.56390 (12976)
  SS BOND              : bond        0.00310 (    6)
  SS BOND              : angle       1.19697 (   12)
  hydrogen bonds       : bond        0.05558 (  504)
  hydrogen bonds       : angle       5.15753 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: R  139 GLU cc_start: 0.5731 (tt0) cc_final: 0.5010 (tp30)
REVERT: R  211 GLN cc_start: 0.7241 (tp-100) cc_final: 0.6479 (mp10)
REVERT: R  397 MET cc_start: 0.8175 (mmp) cc_final: 0.7936 (mmm)
REVERT: A   59 GLN cc_start: 0.6870 (mm-40) cc_final: 0.6043 (tm-30)
REVERT: B   17 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7391 (pt0)
REVERT: B  134 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7238 (mmp-170)
  outliers start: 12
  outliers final: 1
  residues processed: 133
  average time/residue: 0.8166
  time to fit residues: 114.5296
Evaluate side-chains
  111 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 ASN
Chi-restraints excluded: chain B residue   17 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 82 optimal weight:    0.2980
   chunk 5 optimal weight:   50.0000
   chunk 90 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0170
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
R 263 GLN
R 302 ASN
B  17 GLN
B 266 HIS
B 293 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.203497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.147255 restraints weight = 9151.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.75
r_work: 0.3591 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9584  Z= 0.120
  Angle     :  0.510   6.044  12988  Z= 0.281
  Chirality :  0.041   0.142   1424
  Planarity :  0.004   0.057   1656
  Dihedral  :  4.529  23.841   1281
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.70 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.24), residues: 1150
  helix:  2.27 (0.23), residues: 468
  sheet:  0.41 (0.33), residues: 221
  loop :  0.06 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 380 
 TYR   0.029   0.002   TYR R 148 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.020   0.002   TRP R  33 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9578)
  covalent geometry    : angle       0.50961 (12976)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       1.02474 (   12)
  hydrogen bonds       : bond        0.04718 (  504)
  hydrogen bonds       : angle       4.75805 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.372 
Fit side-chains
REVERT: R  211 GLN cc_start: 0.7290 (tp-100) cc_final: 0.6595 (mp10)
REVERT: R  291 TYR cc_start: 0.7886 (m-80) cc_final: 0.7669 (m-10)
REVERT: R  397 MET cc_start: 0.8166 (mmp) cc_final: 0.7895 (mmm)
REVERT: A   59 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6178 (tm-30)
REVERT: B   96 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7770 (mtm110)
REVERT: B  134 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7202 (mmp-170)
REVERT: G   47 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7962 (pt0)
  outliers start: 10
  outliers final: 1
  residues processed: 115
  average time/residue: 0.8000
  time to fit residues: 96.9451
Evaluate side-chains
  106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 ASN
Chi-restraints excluded: chain G residue   47 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 73 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
R 263 GLN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.200373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.144980 restraints weight = 9120.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 1.82
r_work: 0.3538 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9584  Z= 0.179
  Angle     :  0.576   5.882  12988  Z= 0.318
  Chirality :  0.044   0.145   1424
  Planarity :  0.005   0.056   1656
  Dihedral  :  4.888  25.974   1281
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  8.61 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.24), residues: 1150
  helix:  2.20 (0.23), residues: 469
  sheet:  0.42 (0.33), residues: 229
  loop :  0.06 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 380 
 TYR   0.027   0.002   TYR R 148 
 PHE   0.015   0.002   PHE R 369 
 TRP   0.020   0.002   TRP R  33 
 HIS   0.008   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9578)
  covalent geometry    : angle       0.57552 (12976)
  SS BOND              : bond        0.00393 (    6)
  SS BOND              : angle       1.11751 (   12)
  hydrogen bonds       : bond        0.05190 (  504)
  hydrogen bonds       : angle       4.88685 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.377 
Fit side-chains
REVERT: R  105 THR cc_start: 0.4723 (OUTLIER) cc_final: 0.4339 (t)
REVERT: R  211 GLN cc_start: 0.7318 (tp-100) cc_final: 0.6623 (mp10)
REVERT: R  291 TYR cc_start: 0.7939 (m-80) cc_final: 0.7664 (m-10)
REVERT: R  372 ASP cc_start: 0.7330 (t0) cc_final: 0.7101 (t0)
REVERT: R  397 MET cc_start: 0.8223 (mmp) cc_final: 0.7999 (mmm)
REVERT: B  217 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7975 (pmm)
  outliers start: 18
  outliers final: 9
  residues processed: 114
  average time/residue: 0.8019
  time to fit residues: 96.0690
Evaluate side-chains
  112 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  347 CYS
Chi-restraints excluded: chain R residue  407 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 95 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.200075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.142434 restraints weight = 9081.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.41
r_work: 0.3571 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9584  Z= 0.161
  Angle     :  0.555   5.809  12988  Z= 0.306
  Chirality :  0.043   0.139   1424
  Planarity :  0.004   0.054   1656
  Dihedral  :  4.841  26.755   1281
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.59 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.24), residues: 1150
  helix:  2.22 (0.23), residues: 470
  sheet:  0.49 (0.33), residues: 227
  loop :  0.05 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 134 
 TYR   0.025   0.002   TYR R 148 
 PHE   0.014   0.002   PHE B 151 
 TRP   0.022   0.002   TRP R  33 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9578)
  covalent geometry    : angle       0.55456 (12976)
  SS BOND              : bond        0.00346 (    6)
  SS BOND              : angle       1.06237 (   12)
  hydrogen bonds       : bond        0.04957 (  504)
  hydrogen bonds       : angle       4.79006 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.323 
Fit side-chains
REVERT: R  105 THR cc_start: 0.4537 (OUTLIER) cc_final: 0.4166 (t)
REVERT: R  211 GLN cc_start: 0.7355 (tp-100) cc_final: 0.6650 (mp10)
REVERT: R  372 ASP cc_start: 0.7266 (t0) cc_final: 0.7058 (t0)
REVERT: R  397 MET cc_start: 0.8150 (mmp) cc_final: 0.7923 (mmm)
REVERT: B  134 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7383 (mmp-170)
REVERT: B  217 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7961 (pmm)
  outliers start: 18
  outliers final: 9
  residues processed: 111
  average time/residue: 0.7661
  time to fit residues: 89.4613
Evaluate side-chains
  109 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  407 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 84 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
B 266 HIS
** G  59 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 = 0.4300 r_free = 0.4300 target = 0.201196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.149709 restraints weight = 9135.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.77
r_work: 0.3573 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9584  Z= 0.133
  Angle     :  0.520   6.690  12988  Z= 0.286
  Chirality :  0.042   0.139   1424
  Planarity :  0.004   0.052   1656
  Dihedral  :  4.667  25.582   1281
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.48 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.25), residues: 1150
  helix:  2.35 (0.23), residues: 470
  sheet:  0.53 (0.33), residues: 227
  loop :  0.04 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 380 
 TYR   0.024   0.002   TYR R 148 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.024   0.002   TRP R  33 
 HIS   0.005   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9578)
  covalent geometry    : angle       0.51895 (12976)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       1.00244 (   12)
  hydrogen bonds       : bond        0.04596 (  504)
  hydrogen bonds       : angle       4.64393 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.352 
Fit side-chains
REVERT: R  105 THR cc_start: 0.4682 (OUTLIER) cc_final: 0.4286 (t)
REVERT: R  211 GLN cc_start: 0.7408 (tp-100) cc_final: 0.6692 (mp10)
REVERT: R  291 TYR cc_start: 0.7821 (m-80) cc_final: 0.7570 (m-10)
REVERT: R  397 MET cc_start: 0.8140 (mmp) cc_final: 0.7920 (mmm)
REVERT: B  134 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7308 (mmp-170)
REVERT: B  217 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7996 (pmm)
  outliers start: 20
  outliers final: 13
  residues processed: 115
  average time/residue: 0.7028
  time to fit residues: 85.1517
Evaluate side-chains
  113 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 4 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 107 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
A 213 GLN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.200991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.148762 restraints weight = 9138.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 1.76
r_work: 0.3568 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9584  Z= 0.135
  Angle     :  0.520   5.527  12988  Z= 0.287
  Chirality :  0.042   0.139   1424
  Planarity :  0.004   0.051   1656
  Dihedral  :  4.555  23.676   1279
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.58 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.25), residues: 1150
  helix:  2.38 (0.23), residues: 470
  sheet:  0.59 (0.33), residues: 228
  loop :  0.08 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 380 
 TYR   0.024   0.002   TYR R 148 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.026   0.002   TRP R  33 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9578)
  covalent geometry    : angle       0.51985 (12976)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       0.98409 (   12)
  hydrogen bonds       : bond        0.04581 (  504)
  hydrogen bonds       : angle       4.63430 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.378 
Fit side-chains
REVERT: R  105 THR cc_start: 0.4594 (OUTLIER) cc_final: 0.4191 (t)
REVERT: R  211 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6691 (mp10)
REVERT: R  291 TYR cc_start: 0.7775 (m-80) cc_final: 0.7517 (m-10)
REVERT: R  397 MET cc_start: 0.8149 (mmp) cc_final: 0.7933 (mmm)
REVERT: R  418 GLU cc_start: 0.5833 (tp30) cc_final: 0.5565 (tp30)
REVERT: A   58 LYS cc_start: 0.7309 (tttt) cc_final: 0.6903 (mttt)
REVERT: B   46 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7951 (mmt-90)
REVERT: B   96 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7808 (mtm110)
REVERT: B  215 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7843 (mm-30)
REVERT: B  217 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8032 (pmm)
  outliers start: 21
  outliers final: 13
  residues processed: 115
  average time/residue: 0.8125
  time to fit residues: 98.5822
Evaluate side-chains
  118 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  259 VAL
Chi-restraints excluded: chain R residue  347 CYS
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    0.2980
   chunk 1 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0170
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
B 266 HIS
G  44 HIS
** G  59 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 = 0.4317 r_free = 0.4317 target = 0.203095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.151802 restraints weight = 9185.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.78
r_work: 0.3606 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9584  Z= 0.106
  Angle     :  0.487   7.713  12988  Z= 0.267
  Chirality :  0.041   0.138   1424
  Planarity :  0.004   0.051   1656
  Dihedral  :  4.278  22.977   1279
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.57 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.25), residues: 1150
  helix:  2.54 (0.23), residues: 470
  sheet:  0.57 (0.33), residues: 227
  loop :  0.13 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 134 
 TYR   0.023   0.001   TYR R 148 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.029   0.002   TRP R  33 
 HIS   0.004   0.001   HIS R 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 9578)
  covalent geometry    : angle       0.48627 (12976)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       0.89369 (   12)
  hydrogen bonds       : bond        0.04109 (  504)
  hydrogen bonds       : angle       4.43226 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.433 
Fit side-chains
REVERT: R  105 THR cc_start: 0.4703 (OUTLIER) cc_final: 0.4295 (t)
REVERT: R  211 GLN cc_start: 0.7421 (tp-100) cc_final: 0.6749 (mp10)
REVERT: R  291 TYR cc_start: 0.7672 (m-80) cc_final: 0.7406 (m-10)
REVERT: R  397 MET cc_start: 0.8134 (mmp) cc_final: 0.7919 (mmm)
REVERT: A   58 LYS cc_start: 0.7413 (tttt) cc_final: 0.7045 (mttt)
REVERT: B   96 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7845 (mtm110)
REVERT: B  134 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7325 (mmp-170)
  outliers start: 14
  outliers final: 10
  residues processed: 118
  average time/residue: 0.6954
  time to fit residues: 86.8380
Evaluate side-chains
  113 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  347 CYS
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0470
   chunk 35 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
R 302 ASN
B 220 GLN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.202634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146443 restraints weight = 9175.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.77
r_work: 0.3584 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9584  Z= 0.111
  Angle     :  0.490   6.375  12988  Z= 0.269
  Chirality :  0.041   0.137   1424
  Planarity :  0.004   0.053   1656
  Dihedral  :  4.298  22.897   1279
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.97 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.25), residues: 1150
  helix:  2.56 (0.23), residues: 471
  sheet:  0.57 (0.33), residues: 229
  loop :  0.14 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 134 
 TYR   0.023   0.001   TYR R 148 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.031   0.002   TRP R  33 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9578)
  covalent geometry    : angle       0.48952 (12976)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.89139 (   12)
  hydrogen bonds       : bond        0.04178 (  504)
  hydrogen bonds       : angle       4.42196 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.394 
Fit side-chains
REVERT: R   33 TRP cc_start: 0.6982 (t60) cc_final: 0.6750 (t60)
REVERT: R  105 THR cc_start: 0.4712 (OUTLIER) cc_final: 0.4318 (t)
REVERT: R  211 GLN cc_start: 0.7451 (tp-100) cc_final: 0.6763 (mp10)
REVERT: R  291 TYR cc_start: 0.7669 (m-80) cc_final: 0.7425 (m-10)
REVERT: A   58 LYS cc_start: 0.7344 (tttt) cc_final: 0.6904 (mttt)
REVERT: B   96 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7867 (mtm110)
REVERT: B  134 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7294 (mmp-170)
  outliers start: 15
  outliers final: 9
  residues processed: 113
  average time/residue: 0.7461
  time to fit residues: 89.0484
Evaluate side-chains
  112 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
R 302 ASN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.200057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.147706 restraints weight = 9095.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.77
r_work: 0.3552 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9584  Z= 0.160
  Angle     :  0.559   6.427  12988  Z= 0.307
  Chirality :  0.043   0.142   1424
  Planarity :  0.005   0.051   1656
  Dihedral  :  4.624  23.553   1279
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.46 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.25), residues: 1150
  helix:  2.37 (0.23), residues: 471
  sheet:  0.56 (0.33), residues: 230
  loop :  0.12 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 134 
 TYR   0.024   0.002   TYR R 148 
 PHE   0.014   0.002   PHE B 151 
 TRP   0.034   0.002   TRP R 420 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9578)
  covalent geometry    : angle       0.55878 (12976)
  SS BOND              : bond        0.00345 (    6)
  SS BOND              : angle       1.01689 (   12)
  hydrogen bonds       : bond        0.04772 (  504)
  hydrogen bonds       : angle       4.65411 ( 1425)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.284 
Fit side-chains
REVERT: R   33 TRP cc_start: 0.6998 (t60) cc_final: 0.6797 (t60)
REVERT: R  105 THR cc_start: 0.4757 (OUTLIER) cc_final: 0.4363 (t)
REVERT: R  211 GLN cc_start: 0.7445 (tp-100) cc_final: 0.6744 (mp10)
REVERT: R  291 TYR cc_start: 0.7710 (m-80) cc_final: 0.7446 (m-10)
REVERT: P   12 LYS cc_start: 0.7785 (mttt) cc_final: 0.7491 (mttp)
REVERT: A   28 LYS cc_start: 0.7705 (pptt) cc_final: 0.7132 (pttp)
REVERT: A   58 LYS cc_start: 0.7376 (tttt) cc_final: 0.6885 (mttt)
REVERT: B   96 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7835 (mtm110)
REVERT: B  134 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7328 (mmp-170)
  outliers start: 12
  outliers final: 10
  residues processed: 114
  average time/residue: 0.6722
  time to fit residues: 80.7248
Evaluate side-chains
  113 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 140 GLN
R 302 ASN
B 220 GLN
B 266 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.201958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.145507 restraints weight = 9115.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 1.79
r_work: 0.3580 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9584  Z= 0.115
  Angle     :  0.511   9.048  12988  Z= 0.278
  Chirality :  0.041   0.139   1424
  Planarity :  0.004   0.050   1656
  Dihedral  :  4.384  23.329   1279
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.46 %
    Favored  : 86.25 %
  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 aren not related in a simple way.
  whole:  1.77 (0.25), residues: 1150
  helix:  2.50 (0.23), residues: 471
  sheet:  0.58 (0.33), residues: 229
  loop :  0.13 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 134 
 TYR   0.023   0.001   TYR R 148 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.033   0.002   TRP R 420 
 HIS   0.005   0.001   HIS R 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9578)
  covalent geometry    : angle       0.51013 (12976)
  SS BOND              : bond        0.00235 (    6)
  SS BOND              : angle       0.89458 (   12)
  hydrogen bonds       : bond        0.04239 (  504)
  hydrogen bonds       : angle       4.47227 ( 1425)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4729.10 seconds
wall clock time: 81 minutes 4.17 seconds (4864.17 seconds total)