Starting phenix.real_space_refine
on Sat Aug 23 03:46:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j6q_36011/08_2025/8j6q_36011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j6q_36011/08_2025/8j6q_36011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j6q_36011/08_2025/8j6q_36011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j6q_36011/08_2025/8j6q_36011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j6q_36011/08_2025/8j6q_36011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j6q_36011/08_2025/8j6q_36011.cif"
  }
  resolution = 2.6
  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=   0.007
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      69      5.16       5
     C    5876      2.51       5
     N    1554      2.21       5
     O    1688      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9187
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1795
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2420
          Classifications: {'peptide': 295}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284}
    Chain: "R"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 110
          Unusual residues: {'3HR': 1, 'CLR': 2, 'IX8': 1, 'NAG': 1}
          Classifications: {'undetermined': 5, 'water': 1}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.23, per 1000 atoms: 0.24
  Number of scatterers: 9187
  At special positions: 0
  Unit cell: (106.02, 119.04, 113.46, 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      69     16.00
     O    1688      8.00
     N    1554      7.00
     C    5876      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " 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
  Links applied
    NAG-ASN
      " NAG R 405 " - " ASN R  17 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 386.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      38.3% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.616A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.335A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.034A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.607A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.526A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.098A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
    Processing helix  chain 'R' and resid 23 through 54
      removed outlier: 3.877A  pdb=" N   VAL R  27 " --> pdb=" O   ASP R  23 " (cutoff:3.500A)
      Proline residue:  R  31  - end of helix
    Processing helix  chain 'R' and resid 60 through 78
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.671A  pdb=" N   LEU R  83 " --> pdb=" O   CYS R  79 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ARG R  89 " --> pdb=" O   ASP R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 130
      removed outlier: 3.728A  pdb=" N   CYS R 100 " --> pdb=" O   GLY R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 139
      removed outlier: 3.661A  pdb=" N   ILE R 139 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 160
    Processing helix  chain 'R' and resid 161 through 165
      removed outlier: 3.672A  pdb=" N   LYS R 164 " --> pdb=" O   HIS R 161 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS R 165 " --> pdb=" O   LEU R 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 161 through 165'
    Processing helix  chain 'R' and resid 170 through 174
      removed outlier: 4.031A  pdb=" N   GLY R 173 " --> pdb=" O   GLN R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 218
      removed outlier: 3.523A  pdb=" N   ALA R 191 " --> pdb=" O   GLN R 187 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 219 through 222
      removed outlier: 3.644A  pdb=" N   ARG R 222 " --> pdb=" O   GLN R 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 219 through 222'
    Processing helix  chain 'R' and resid 223 through 261
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 265 through 267
      No H-bonds generated for 'chain 'R' and resid 265 through 267'
    Processing helix  chain 'R' and resid 268 through 295
      removed outlier: 4.461A  pdb=" N   VAL R 272 " --> pdb=" O   VAL R 268 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR R 283 " --> pdb=" O   THR R 279 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR R 284 " --> pdb=" O   LEU R 280 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 5.945A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.455A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.787A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.458A  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: 6.836A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.066A  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: 3.518A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.657A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.345A  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: 3.672A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.547A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 5.958A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.860A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.525A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12

    448 hydrogen bonds defined for protein.
    1242 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: 1.53

  Time building geometry restraints manager: 1.21 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: 1985
        1.33 -     1.46: 2469
        1.46 -     1.58: 4837
        1.58 -     1.71: 1
        1.71 -     1.83: 100
  Bond restraints: 9392
  Sorted by residual:
  bond pdb=" C2  IX8 R 401 "
       pdb=" C25 IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.522  1.649 -0.127 2.00e-02 2.50e+03 4.01e+01
  bond pdb=" C4  IX8 R 401 "
       pdb=" N3  IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.442 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C2  IX8 R 401 "
       pdb=" N3  IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.451  1.538 -0.087 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" C15 IX8 R 401 "
       pdb=" C16 IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.460  1.545 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C11 IX8 R 401 "
       pdb=" N10 IX8 R 401 "
    ideal  model  delta    sigma   weight residual
    1.359  1.442 -0.083 2.00e-02 2.50e+03 1.74e+01
  ... (remaining 9387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 12443
        2.00 -     4.00: 207
        4.00 -     6.00: 53
        6.00 -     8.01: 12
        8.01 -    10.01: 4
  Bond angle restraints: 12719
  Sorted by residual:
  angle pdb=" N   CYS R  18 "
        pdb=" CA  CYS R  18 "
        pdb=" C   CYS R  18 "
      ideal   model   delta    sigma   weight residual
     108.24  113.37   -5.13 1.32e+00 5.74e-01 1.51e+01
  angle pdb=" N   VAL S  64 "
        pdb=" CA  VAL S  64 "
        pdb=" C   VAL S  64 "
      ideal   model   delta    sigma   weight residual
     113.20  109.70    3.50 9.60e-01 1.09e+00 1.33e+01
  angle pdb=" C   ASP S  73 "
        pdb=" N   ASP S  74 "
        pdb=" CA  ASP S  74 "
      ideal   model   delta    sigma   weight residual
     120.06  124.17   -4.11 1.19e+00 7.06e-01 1.19e+01
  angle pdb=" CA  GLN R 170 "
        pdb=" CB  GLN R 170 "
        pdb=" CG  GLN R 170 "
      ideal   model   delta    sigma   weight residual
     114.10  120.97   -6.87 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" N   GLU A  25 "
        pdb=" CA  GLU A  25 "
        pdb=" CB  GLU A  25 "
      ideal   model   delta    sigma   weight residual
     110.28  115.52   -5.24 1.55e+00 4.16e-01 1.14e+01
  ... (remaining 12714 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5174
       17.82 -    35.64: 422
       35.64 -    53.46: 55
       53.46 -    71.28: 21
       71.28 -    89.10: 6
  Dihedral angle restraints: 5678
    sinusoidal: 2343
      harmonic: 3335
  Sorted by residual:
  dihedral pdb=" CB  CYS R  18 "
           pdb=" SG  CYS R  18 "
           pdb=" SG  CYS R 183 "
           pdb=" CB  CYS R 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.96   40.04     1      1.00e+01 1.00e-02 2.25e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+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  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 5675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1322
       0.089 -    0.179: 101
       0.179 -    0.268: 6
       0.268 -    0.357: 0
       0.357 -    0.446: 1
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" C2  IX8 R 401 "
            pdb=" C1  IX8 R 401 "
            pdb=" C25 IX8 R 401 "
            pdb=" N3  IX8 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.86   -0.45 2.00e-01 2.50e+01 4.98e+00
  chirality pdb=" C3  3HR R 403 "
            pdb=" C2  3HR R 403 "
            pdb=" C4  3HR R 403 "
            pdb=" O2  3HR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.58    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.73   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.049 5.00e-02 4.00e+02   7.45e-02 8.87e+00
        pdb=" N   PRO S  75 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO B 236 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R  38 "    0.006 2.00e-02 2.50e+03   1.36e-02 3.23e+00
        pdb=" CG  PHE R  38 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE R  38 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE R  38 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE R  38 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE R  38 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE R  38 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 534
        2.73 -     3.27: 8950
        3.27 -     3.82: 16278
        3.82 -     4.36: 20262
        4.36 -     4.90: 34023
  Nonbonded interactions: 80047
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.266 3.040
  ... (remaining 80042 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:             0.940
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.580
  Find NCS groups from input model:        0.030
  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:8.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
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   0.127   9398  Z= 0.219
  Angle     :  0.696  10.008  12732  Z= 0.355
  Chirality :  0.048   0.446   1430
  Planarity :  0.004   0.074   1595
  Dihedral  : 13.239  89.104   3507
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.40 (0.25), residues: 1137
  helix:  1.12 (0.26), residues: 384
  sheet:  0.12 (0.30), residues: 283
  loop : -0.23 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.025   0.002   TYR S 190 
 PHE   0.028   0.002   PHE R  38 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9392)
  covalent geometry    : angle       0.69478 (12719)
  SS BOND              : bond        0.00501 (    5)
  SS BOND              : angle       1.21837 (   10)
  hydrogen bonds       : bond        0.16774 (  443)
  hydrogen bonds       : angle       6.70476 ( 1242)
  link_NAG-ASN         : bond        0.00100 (    1)
  link_NAG-ASN         : angle       1.51826 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.256 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.4591
  time to fit residues: 77.5914
Evaluate side-chains
  142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.1980
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.161617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.121930 restraints weight = 9205.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.07
r_work: 0.3083 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9398  Z= 0.134
  Angle     :  0.529   8.244  12732  Z= 0.287
  Chirality :  0.042   0.182   1430
  Planarity :  0.004   0.066   1595
  Dihedral  :  6.966  89.035   1415
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  8.74 %
    Favored  : 90.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.74 (0.25), residues: 1137
  helix:  1.76 (0.27), residues: 381
  sheet:  0.04 (0.30), residues: 279
  loop : -0.18 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S  72 
 TYR   0.024   0.001   TYR S 190 
 PHE   0.013   0.001   PHE R  38 
 TRP   0.018   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9392)
  covalent geometry    : angle       0.52800 (12719)
  SS BOND              : bond        0.00487 (    5)
  SS BOND              : angle       1.17121 (   10)
  hydrogen bonds       : bond        0.04239 (  443)
  hydrogen bonds       : angle       4.83638 ( 1242)
  link_NAG-ASN         : bond        0.00068 (    1)
  link_NAG-ASN         : angle       1.78795 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.255 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.7762 (mpp-170) cc_final: 0.7487 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7829 (mtt-85)
REVERT: G   36 ASP cc_start: 0.8222 (m-30) cc_final: 0.7973 (m-30)
REVERT: S  160 ARG cc_start: 0.7581 (mtm110) cc_final: 0.6754 (mmm160)
REVERT: R  102 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6942 (mm)
REVERT: R  110 ASN cc_start: 0.8553 (m110) cc_final: 0.8283 (m110)
  outliers start: 12
  outliers final: 2
  residues processed: 150
  average time/residue: 0.4891
  time to fit residues: 77.9800
Evaluate side-chains
  144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
A 333 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.160603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.120817 restraints weight = 9239.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.97
r_work: 0.3061 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9398  Z= 0.134
  Angle     :  0.517   7.168  12732  Z= 0.279
  Chirality :  0.042   0.183   1430
  Planarity :  0.004   0.064   1595
  Dihedral  :  6.548  84.085   1415
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.16 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.79 (0.26), residues: 1137
  helix:  1.93 (0.27), residues: 381
  sheet: -0.04 (0.29), residues: 290
  loop : -0.19 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.010   0.001   PHE A 189 
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9392)
  covalent geometry    : angle       0.51523 (12719)
  SS BOND              : bond        0.00487 (    5)
  SS BOND              : angle       1.13901 (   10)
  hydrogen bonds       : bond        0.04085 (  443)
  hydrogen bonds       : angle       4.69076 ( 1242)
  link_NAG-ASN         : bond        0.00047 (    1)
  link_NAG-ASN         : angle       1.69220 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7327 (mm-30)
REVERT: A  240 MET cc_start: 0.6145 (tpp) cc_final: 0.5779 (tpp)
REVERT: B   46 ARG cc_start: 0.7899 (mpp-170) cc_final: 0.7626 (mtm-85)
REVERT: G   36 ASP cc_start: 0.8301 (m-30) cc_final: 0.8007 (m-30)
REVERT: S   89 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7666 (pp20)
REVERT: R  102 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7103 (mm)
REVERT: R  110 ASN cc_start: 0.8549 (m110) cc_final: 0.8316 (m110)
REVERT: R  253 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7035 (tpm170)
  outliers start: 10
  outliers final: 3
  residues processed: 150
  average time/residue: 0.4913
  time to fit residues: 78.6579
Evaluate side-chains
  142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0000
   chunk 20 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 333 GLN
B 268 ASN
B 340 ASN
S 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.162615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.121740 restraints weight = 9225.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.01
r_work: 0.3094 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9398  Z= 0.117
  Angle     :  0.493   7.124  12732  Z= 0.267
  Chirality :  0.041   0.175   1430
  Planarity :  0.004   0.062   1595
  Dihedral  :  6.193  77.400   1415
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.17 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.83 (0.26), residues: 1137
  helix:  2.05 (0.27), residues: 381
  sheet: -0.19 (0.29), residues: 280
  loop : -0.12 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  62 
 TYR   0.024   0.001   TYR S 190 
 PHE   0.020   0.001   PHE R  38 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9392)
  covalent geometry    : angle       0.49129 (12719)
  SS BOND              : bond        0.00456 (    5)
  SS BOND              : angle       1.00688 (   10)
  hydrogen bonds       : bond        0.03777 (  443)
  hydrogen bonds       : angle       4.52581 ( 1242)
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.65650 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7969 (m-30) cc_final: 0.7765 (m-30)
REVERT: A  240 MET cc_start: 0.6186 (tpp) cc_final: 0.5831 (tpp)
REVERT: A  275 GLU cc_start: 0.7356 (tp30) cc_final: 0.7006 (tp30)
REVERT: B   46 ARG cc_start: 0.7831 (mpp-170) cc_final: 0.7535 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7825 (mtt-85)
REVERT: G   36 ASP cc_start: 0.8216 (m-30) cc_final: 0.7891 (m-30)
REVERT: S   89 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7535 (pp20)
REVERT: R   42 LEU cc_start: 0.7873 (tp) cc_final: 0.7664 (tp)
REVERT: R  102 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6960 (mm)
REVERT: R  110 ASN cc_start: 0.8445 (m110) cc_final: 0.8216 (m110)
REVERT: R  253 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.6941 (tpm170)
  outliers start: 15
  outliers final: 5
  residues processed: 146
  average time/residue: 0.5020
  time to fit residues: 78.0312
Evaluate side-chains
  145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 89 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0060
   chunk 107 optimal weight:    0.6980
   chunk 102 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.162358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.121565 restraints weight = 9207.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.00
r_work: 0.3092 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9398  Z= 0.119
  Angle     :  0.492   7.125  12732  Z= 0.266
  Chirality :  0.041   0.178   1430
  Planarity :  0.004   0.061   1595
  Dihedral  :  6.005  72.059   1415
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.37 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.84 (0.26), residues: 1137
  helix:  2.09 (0.27), residues: 381
  sheet: -0.22 (0.29), residues: 278
  loop : -0.11 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  62 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.015   0.001   PHE R  38 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9392)
  covalent geometry    : angle       0.49040 (12719)
  SS BOND              : bond        0.00450 (    5)
  SS BOND              : angle       0.99314 (   10)
  hydrogen bonds       : bond        0.03713 (  443)
  hydrogen bonds       : angle       4.49772 ( 1242)
  link_NAG-ASN         : bond        0.00019 (    1)
  link_NAG-ASN         : angle       1.59562 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7974 (m-30) cc_final: 0.7773 (m-30)
REVERT: A  240 MET cc_start: 0.6049 (tpp) cc_final: 0.5809 (tpp)
REVERT: B   46 ARG cc_start: 0.7824 (mpp-170) cc_final: 0.7515 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7833 (mtt-85)
REVERT: G   36 ASP cc_start: 0.8208 (m-30) cc_final: 0.7874 (m-30)
REVERT: S   89 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7507 (pp20)
REVERT: R  102 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6982 (mm)
REVERT: R  110 ASN cc_start: 0.8444 (m110) cc_final: 0.8222 (m110)
REVERT: R  253 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.6916 (tpm170)
  outliers start: 14
  outliers final: 3
  residues processed: 147
  average time/residue: 0.5059
  time to fit residues: 78.8022
Evaluate side-chains
  140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9990
   chunk 70 optimal weight:    0.4980
   chunk 73 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  75 GLN
B 259 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.160510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121498 restraints weight = 9211.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.93
r_work: 0.3064 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9398  Z= 0.135
  Angle     :  0.512   7.119  12732  Z= 0.276
  Chirality :  0.042   0.186   1430
  Planarity :  0.004   0.062   1595
  Dihedral  :  5.956  67.757   1415
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.77 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.87 (0.26), residues: 1137
  helix:  2.08 (0.27), residues: 382
  sheet: -0.27 (0.29), residues: 281
  loop : -0.03 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  62 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.025   0.001   PHE R  38 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9392)
  covalent geometry    : angle       0.51116 (12719)
  SS BOND              : bond        0.00443 (    5)
  SS BOND              : angle       1.06168 (   10)
  hydrogen bonds       : bond        0.03832 (  443)
  hydrogen bonds       : angle       4.53449 ( 1242)
  link_NAG-ASN         : bond        0.00029 (    1)
  link_NAG-ASN         : angle       1.42735 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  240 MET cc_start: 0.5924 (tpp) cc_final: 0.5668 (tpp)
REVERT: B   46 ARG cc_start: 0.7922 (mpp-170) cc_final: 0.7641 (mtm-85)
REVERT: B   96 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7948 (mtt-85)
REVERT: B  259 GLN cc_start: 0.7918 (tt0) cc_final: 0.7647 (tt0)
REVERT: G   36 ASP cc_start: 0.8394 (m-30) cc_final: 0.8080 (m-30)
REVERT: S   89 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7592 (pp20)
REVERT: R  102 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7242 (mm)
REVERT: R  253 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7057 (tpm170)
  outliers start: 17
  outliers final: 7
  residues processed: 146
  average time/residue: 0.5358
  time to fit residues: 82.8924
Evaluate side-chains
  141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  222 ARG
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0040
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  75 GLN
B 268 ASN
B 340 ASN
** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.161815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120711 restraints weight = 9158.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.97
r_work: 0.3069 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9398  Z= 0.126
  Angle     :  0.507   7.107  12732  Z= 0.274
  Chirality :  0.041   0.179   1430
  Planarity :  0.004   0.062   1595
  Dihedral  :  5.853  64.438   1415
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.18 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.89 (0.26), residues: 1137
  helix:  2.13 (0.27), residues: 380
  sheet: -0.25 (0.29), residues: 279
  loop : -0.04 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.020   0.001   PHE R  38 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9392)
  covalent geometry    : angle       0.50631 (12719)
  SS BOND              : bond        0.00422 (    5)
  SS BOND              : angle       1.02556 (   10)
  hydrogen bonds       : bond        0.03742 (  443)
  hydrogen bonds       : angle       4.51674 ( 1242)
  link_NAG-ASN         : bond        0.00012 (    1)
  link_NAG-ASN         : angle       1.39413 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.303 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.7871 (mpp-170) cc_final: 0.7555 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7846 (tt0) cc_final: 0.7563 (tt0)
REVERT: G   21 MET cc_start: 0.6276 (ttt) cc_final: 0.5685 (ttt)
REVERT: G   36 ASP cc_start: 0.8315 (m-30) cc_final: 0.7979 (m-30)
REVERT: S   89 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7525 (pp20)
REVERT: R  102 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7084 (mm)
REVERT: R  216 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7455 (mtt-85)
REVERT: R  253 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7031 (tpm170)
  outliers start: 16
  outliers final: 7
  residues processed: 137
  average time/residue: 0.5189
  time to fit residues: 75.3250
Evaluate side-chains
  138 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  75 GLN
B 268 ASN
B 340 ASN
** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.160758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121253 restraints weight = 9173.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.89
r_work: 0.3074 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9398  Z= 0.132
  Angle     :  0.513   7.124  12732  Z= 0.277
  Chirality :  0.041   0.183   1430
  Planarity :  0.004   0.062   1595
  Dihedral  :  5.821  62.046   1415
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.38 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.86 (0.25), residues: 1137
  helix:  2.08 (0.27), residues: 381
  sheet: -0.29 (0.29), residues: 281
  loop : -0.02 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.018   0.001   PHE R  38 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9392)
  covalent geometry    : angle       0.51234 (12719)
  SS BOND              : bond        0.00429 (    5)
  SS BOND              : angle       1.09668 (   10)
  hydrogen bonds       : bond        0.03738 (  443)
  hydrogen bonds       : angle       4.51491 ( 1242)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       1.36387 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.266 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.7870 (mpp-170) cc_final: 0.7562 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7939 (tt0) cc_final: 0.7677 (tt0)
REVERT: G   21 MET cc_start: 0.6240 (ttt) cc_final: 0.5682 (ttt)
REVERT: G   36 ASP cc_start: 0.8243 (m-30) cc_final: 0.7914 (m-30)
REVERT: S   89 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7561 (pp20)
REVERT: R  102 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7194 (mm)
REVERT: R  216 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7487 (mtt-85)
REVERT: R  253 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7058 (tpm170)
  outliers start: 14
  outliers final: 9
  residues processed: 142
  average time/residue: 0.5431
  time to fit residues: 81.8216
Evaluate side-chains
  142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  222 ARG
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Chi-restraints excluded: chain R residue  287 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0050
   chunk 11 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 108 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  75 GLN
B 268 ASN
B 340 ASN
S 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.160972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119903 restraints weight = 9124.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.97
r_work: 0.3060 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9398  Z= 0.135
  Angle     :  0.523   7.120  12732  Z= 0.281
  Chirality :  0.042   0.188   1430
  Planarity :  0.004   0.062   1595
  Dihedral  :  5.802  60.487   1415
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.38 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.84 (0.26), residues: 1137
  helix:  2.03 (0.27), residues: 382
  sheet: -0.30 (0.29), residues: 281
  loop : -0.01 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.026   0.001   TYR S 190 
 PHE   0.030   0.001   PHE R  38 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9392)
  covalent geometry    : angle       0.52239 (12719)
  SS BOND              : bond        0.00427 (    5)
  SS BOND              : angle       1.08773 (   10)
  hydrogen bonds       : bond        0.03777 (  443)
  hydrogen bonds       : angle       4.54505 ( 1242)
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       1.35985 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  248 LYS cc_start: 0.7631 (mttt) cc_final: 0.7348 (mtpt)
REVERT: B   46 ARG cc_start: 0.7876 (mpp-170) cc_final: 0.7541 (mtm-85)
REVERT: G   21 MET cc_start: 0.6136 (ttt) cc_final: 0.5603 (ttt)
REVERT: G   36 ASP cc_start: 0.8223 (m-30) cc_final: 0.7853 (m-30)
REVERT: S   89 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7532 (pp20)
REVERT: R  102 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7134 (mm)
REVERT: R  216 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7489 (mtt-85)
REVERT: R  253 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7030 (tpm170)
  outliers start: 17
  outliers final: 10
  residues processed: 141
  average time/residue: 0.5231
  time to fit residues: 78.1603
Evaluate side-chains
  143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  222 ARG
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Chi-restraints excluded: chain R residue  287 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0170
   chunk 74 optimal weight:    5.9990
   chunk 94 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0010
   chunk 77 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7226

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  75 GLN
B 259 GLN
B 268 ASN
B 340 ASN
S 186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.161792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120661 restraints weight = 9160.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.01
r_work: 0.3069 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9398  Z= 0.127
  Angle     :  0.540  13.101  12732  Z= 0.284
  Chirality :  0.042   0.187   1430
  Planarity :  0.004   0.061   1595
  Dihedral  :  6.085  59.711   1415
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.88 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.87 (0.26), residues: 1137
  helix:  2.05 (0.27), residues: 382
  sheet: -0.26 (0.29), residues: 279
  loop : -0.01 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.026   0.001   TYR S 190 
 PHE   0.029   0.001   PHE R  38 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9392)
  covalent geometry    : angle       0.51968 (12719)
  SS BOND              : bond        0.00412 (    5)
  SS BOND              : angle       0.82620 (   10)
  hydrogen bonds       : bond        0.03713 (  443)
  hydrogen bonds       : angle       4.52772 ( 1242)
  link_NAG-ASN         : bond        0.00610 (    1)
  link_NAG-ASN         : angle       9.42468 (    3)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.363 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.7899 (mpp-170) cc_final: 0.7559 (mtm-85)
REVERT: G   36 ASP cc_start: 0.8216 (m-30) cc_final: 0.7892 (m-30)
REVERT: S   89 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7513 (pp20)
REVERT: R  102 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7182 (mm)
REVERT: R  216 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7498 (mtt-85)
REVERT: R  253 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7028 (tpm170)
  outliers start: 13
  outliers final: 7
  residues processed: 137
  average time/residue: 0.5672
  time to fit residues: 82.4829
Evaluate side-chains
  142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain R residue  102 LEU
Chi-restraints excluded: chain R residue  159 THR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  271 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0270
   chunk 71 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0470
   chunk 93 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  75 GLN
B 268 ASN
B 340 ASN
** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.162981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.122187 restraints weight = 9078.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.00
r_work: 0.3097 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9398  Z= 0.117
  Angle     :  0.520  10.345  12732  Z= 0.277
  Chirality :  0.041   0.177   1430
  Planarity :  0.004   0.061   1595
  Dihedral  :  5.739  59.687   1415
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.18 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.90 (0.26), residues: 1137
  helix:  2.09 (0.27), residues: 382
  sheet: -0.24 (0.29), residues: 282
  loop :  0.01 (0.31), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.025   0.001   TYR S 190 
 PHE   0.025   0.001   PHE R  38 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9392)
  covalent geometry    : angle       0.50673 (12719)
  SS BOND              : bond        0.00360 (    5)
  SS BOND              : angle       0.80440 (   10)
  hydrogen bonds       : bond        0.03598 (  443)
  hydrogen bonds       : angle       4.47242 ( 1242)
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       7.67777 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3126.42 seconds
wall clock time: 53 minutes 57.80 seconds (3237.80 seconds total)