Starting phenix.real_space_refine
on Tue Feb 11 23:40:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e7b_8997/02_2025/6e7b_8997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e7b_8997/02_2025/6e7b_8997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e7b_8997/02_2025/6e7b_8997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e7b_8997/02_2025/6e7b_8997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e7b_8997/02_2025/6e7b_8997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e7b_8997/02_2025/6e7b_8997.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.204 sd=   1.216
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      48      5.16       5
     C    4259      2.51       5
     N    1155      2.21       5
     O    1304      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6774
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3350
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 19, 'TRANS': 406}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3358
          Classifications: {'peptide': 428}
          Link IDs: {'PTRANS': 20, 'TRANS': 407}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.75, per 1000 atoms: 1.00
  Number of scatterers: 6774
  At special positions: 0
  Unit cell: (72, 70, 108, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       6     15.00
     Mg      2     11.99
     O    1304      8.00
     N    1155      7.00
     C    4259      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 867.0 milliseconds
  

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      51.4% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 28
      removed outlier: 3.533A  pdb=" N   VAL B  23 " --> pdb=" O   LYS B  19 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE B  24 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASP B  26 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 4.291A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 79
      removed outlier: 3.526A  pdb=" N   SER B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 106 through 127
      removed outlier: 3.536A  pdb=" N   ALA B 110 " --> pdb=" O   TYR B 106 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU B 125 " --> pdb=" O   ARG B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
      removed outlier: 3.852A  pdb=" N   GLY B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   THR B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE B 152 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 193
      removed outlier: 3.552A  pdb=" N   HIS B 190 " --> pdb=" O   THR B 186 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
      removed outlier: 3.651A  pdb=" N   TYR B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 213 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 3.929A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLY B 235 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   SER B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
      removed outlier: 4.109A  pdb=" N   ASN B 256 " --> pdb=" O   LYS B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.597A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLN B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 391
      removed outlier: 4.050A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ARG B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 402
      removed outlier: 3.898A  pdb=" N   GLU B 401 " --> pdb=" O   TRP B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 426
      removed outlier: 4.038A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 4.161A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.517A  pdb=" N   VAL A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 161
    Processing helix  chain 'A' and resid 182 through 197
      removed outlier: 3.963A  pdb=" N   ILE A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   HIS A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   THR A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.114A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLN A 233 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 277 through 284
      removed outlier: 3.752A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   HIS A 283 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.741A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 4.022A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 402
      removed outlier: 4.109A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.976A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 437
      removed outlier: 4.198A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4
      removed outlier: 7.242A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54
      removed outlier: 3.513A  pdb=" N   VAL B  60 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66
      removed outlier: 6.683A  pdb=" N   LEU B  65 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 138
      removed outlier: 7.176A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200
      removed outlier: 6.811A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 349 through 352
      removed outlier: 8.542A  pdb=" N   LYS B 350 " --> pdb=" O   LEU B 311 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   VAL B 313 " --> pdb=" O   LYS B 350 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   ALA B 352 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   THR B 315 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 68
      removed outlier: 3.572A  pdb=" N   VAL A  66 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A 135 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU A 168 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 56
    Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 354
    Processing sheet with id=AB1, first strand: chain 'A' and resid 351 through 354
      removed outlier: 6.769A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)

    282 hydrogen bonds defined for protein.
    828 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: 1.99

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2227
        1.34 -     1.46: 1241
        1.46 -     1.58: 3372
        1.58 -     1.69: 10
        1.69 -     1.81: 78
  Bond restraints: 6928
  Sorted by residual:
  bond pdb=" O3B G2P B 502 "
       pdb=" PG  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.716  1.607  0.109 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" O1B G2P B 502 "
       pdb=" PB  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.510  1.609 -0.099 2.00e-02 2.50e+03 2.45e+01
  bond pdb=" O2A G2P B 502 "
       pdb=" PA  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.513  1.608 -0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" C5  GTP A 502 "
       pdb=" C6  GTP A 502 "
    ideal  model  delta    sigma   weight residual
    1.390  1.473 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C4  G2P B 502 "
       pdb=" C5  G2P B 502 "
    ideal  model  delta    sigma   weight residual
    1.384  1.465 -0.081 2.00e-02 2.50e+03 1.63e+01
  ... (remaining 6923 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 9258
        2.55 -     5.10: 117
        5.10 -     7.65: 23
        7.65 -    10.19: 9
       10.19 -    12.74: 2
  Bond angle restraints: 9409
  Sorted by residual:
  angle pdb=" PA  G2P B 502 "
        pdb=" C3A G2P B 502 "
        pdb=" PB  G2P B 502 "
      ideal   model   delta    sigma   weight residual
     120.83  108.09   12.74 3.00e+00 1.11e-01 1.80e+01
  angle pdb=" N   TYR B 222 "
        pdb=" CA  TYR B 222 "
        pdb=" C   TYR B 222 "
      ideal   model   delta    sigma   weight residual
     111.28  107.15    4.13 1.09e+00 8.42e-01 1.44e+01
  angle pdb=" C3A G2P B 502 "
        pdb=" PA  G2P B 502 "
        pdb=" O5' G2P B 502 "
      ideal   model   delta    sigma   weight residual
      99.14  109.87  -10.73 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" O1B GTP A 502 "
        pdb=" PB  GTP A 502 "
        pdb=" O2B GTP A 502 "
      ideal   model   delta    sigma   weight residual
     109.50  119.65  -10.15 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" O1A GTP A 502 "
        pdb=" PA  GTP A 502 "
        pdb=" O2A GTP A 502 "
      ideal   model   delta    sigma   weight residual
     109.50  119.32   -9.82 3.00e+00 1.11e-01 1.07e+01
  ... (remaining 9404 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.42: 4076
       31.42 -    62.83: 53
       62.83 -    94.24: 7
       94.24 -   125.66: 1
      125.66 -   157.07: 2
  Dihedral angle restraints: 4139
    sinusoidal: 1670
      harmonic: 2469
  Sorted by residual:
  dihedral pdb=" C5' GTP A 502 "
           pdb=" O5' GTP A 502 "
           pdb=" PA  GTP A 502 "
           pdb=" O3A GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -133.66 -157.07     1      2.00e+01 2.50e-03 4.61e+01
  dihedral pdb=" C8  GTP A 502 "
           pdb=" C1' GTP A 502 "
           pdb=" N9  GTP A 502 "
           pdb=" O4' GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -41.98  146.57     1      2.00e+01 2.50e-03 4.40e+01
  dihedral pdb=" O3B GTP A 502 "
           pdb=" O3A GTP A 502 "
           pdb=" PB  GTP A 502 "
           pdb=" PA  GTP A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  171.08  120.00     1      2.00e+01 2.50e-03 3.60e+01
  ... (remaining 4136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 572
       0.030 -    0.061: 302
       0.061 -    0.091: 101
       0.091 -    0.122: 43
       0.122 -    0.152: 10
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" CA  VAL A 363 "
            pdb=" N   VAL A 363 "
            pdb=" C   VAL A 363 "
            pdb=" CB  VAL A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CB  ILE A 115 "
            pdb=" CA  ILE A 115 "
            pdb=" CG1 ILE A 115 "
            pdb=" CG2 ILE A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CA  ILE B 368 "
            pdb=" N   ILE B 368 "
            pdb=" C   ILE B 368 "
            pdb=" CB  ILE B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.72e-01
  ... (remaining 1025 not shown)

  Planarity restraints: 1221
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  79 "   -0.172 9.50e-02 1.11e+02   7.73e-02 3.68e+00
        pdb=" NE  ARG A  79 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  79 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  79 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  79 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 267 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.38e+00
        pdb=" N   PRO B 268 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 268 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 268 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 356 "    0.028 5.00e-02 4.00e+02   4.23e-02 2.87e+00
        pdb=" N   PRO B 357 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 357 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 357 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1218 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 99
        2.59 -     3.17: 6292
        3.17 -     3.74: 10676
        3.74 -     4.32: 15716
        4.32 -     4.90: 25100
  Nonbonded interactions: 57883
  Sorted by model distance:
  nonbonded pdb="MG    MG B 501 "
            pdb=" O1G G2P B 502 "
     model   vdw
     2.009 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O3G GTP A 502 "
     model   vdw
     2.012 2.170
  nonbonded pdb="MG    MG B 501 "
            pdb=" O1B G2P B 502 "
     model   vdw
     2.049 2.170
  nonbonded pdb="MG    MG B 501 "
            pdb=" O3B G2P B 502 "
     model   vdw
     2.069 2.170
  nonbonded pdb=" OE1 GLU A  71 "
            pdb="MG    MG A 501 "
     model   vdw
     2.099 2.170
  ... (remaining 57878 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 group one per residue
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:             6.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.180
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.109   6928  Z= 0.390
  Angle     :  0.828  12.742   9409  Z= 0.401
  Chirality :  0.043   0.152   1028
  Planarity :  0.004   0.077   1221
  Dihedral  : 11.890 157.073   2555
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.84 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.13 (0.25), residues: 848
  helix: -2.97 (0.19), residues: 352
  sheet: -3.95 (0.43), residues: 93
  loop : -2.06 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  21 
 HIS   0.008   0.001   HIS B   6 
 PHE   0.019   0.002   PHE B 212 
 TYR   0.013   0.002   TYR B 208 
 ARG   0.008   0.001   ARG B 241 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 ASN cc_start: 0.7481 (t0) cc_final: 0.7193 (t0)
REVERT: B  289 LEU cc_start: 0.8010 (mp) cc_final: 0.7745 (mp)
REVERT: B  403 MET cc_start: 0.7705 (tpt) cc_final: 0.6434 (mmm)
REVERT: A   50 ASN cc_start: 0.7276 (t0) cc_final: 0.7027 (t0)
REVERT: A  203 MET cc_start: 0.7696 (mmm) cc_final: 0.7317 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 224
  average time/residue: 0.2372
  time to fit residues: 66.4901
Evaluate side-chains
  135 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.0970
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
B  52 ASN
B 291 GLN
B 329 GLN
A  11 GLN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
A 197 HIS
A 300 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.135203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.117753 restraints weight = 9476.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.121728 restraints weight = 5110.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.124444 restraints weight = 3301.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6928  Z= 0.292
  Angle     :  0.692   6.813   9409  Z= 0.353
  Chirality :  0.047   0.147   1028
  Planarity :  0.005   0.044   1221
  Dihedral  : 10.800 158.363    976
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.25 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.26), residues: 848
  helix: -1.42 (0.23), residues: 362
  sheet: -3.24 (0.45), residues: 89
  loop : -1.73 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  21 
 HIS   0.006   0.001   HIS A  28 
 PHE   0.027   0.003   PHE B  20 
 TYR   0.014   0.002   TYR B 208 
 ARG   0.008   0.001   ARG A  84 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: B   86 ARG cc_start: 0.6982 (mmp-170) cc_final: 0.6349 (tpm170)
REVERT: B  118 ASP cc_start: 0.7372 (m-30) cc_final: 0.7045 (m-30)
REVERT: B  406 MET cc_start: 0.6757 (ptm) cc_final: 0.6387 (tpp)
REVERT: A  103 TYR cc_start: 0.6742 (t80) cc_final: 0.6413 (t80)
REVERT: A  108 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5900 (t80)
REVERT: A  147 SER cc_start: 0.8593 (m) cc_final: 0.8131 (p)
REVERT: A  251 ASP cc_start: 0.6817 (m-30) cc_final: 0.6610 (m-30)
  outliers start: 19
  outliers final: 11
  residues processed: 164
  average time/residue: 0.2012
  time to fit residues: 43.6471
Evaluate side-chains
  132 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  367 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 83 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 68 optimal weight:    0.3980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
A  50 ASN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** 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 = 0.3906 r_free = 0.3906 target = 0.134181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.117455 restraints weight = 9674.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.121254 restraints weight = 5200.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.123915 restraints weight = 3352.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6928  Z= 0.214
  Angle     :  0.615   8.349   9409  Z= 0.312
  Chirality :  0.045   0.141   1028
  Planarity :  0.004   0.037   1221
  Dihedral  : 10.522 166.163    974
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.44 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.27), residues: 848
  helix: -0.75 (0.24), residues: 374
  sheet: -2.75 (0.48), residues: 95
  loop : -1.45 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 105 
 PHE   0.027   0.002   PHE B  20 
 TYR   0.011   0.001   TYR A 399 
 ARG   0.005   0.001   ARG A   2 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8604 (mpp) cc_final: 0.8019 (mpp)
REVERT: B   74 ASP cc_start: 0.8327 (m-30) cc_final: 0.8123 (m-30)
REVERT: B   77 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7935 (mtt-85)
REVERT: B   86 ARG cc_start: 0.7002 (mmp-170) cc_final: 0.5247 (tpt170)
REVERT: B  118 ASP cc_start: 0.7418 (m-30) cc_final: 0.7094 (m-30)
REVERT: B  300 MET cc_start: 0.8579 (ptp) cc_final: 0.8374 (ptp)
REVERT: A  103 TYR cc_start: 0.7061 (t80) cc_final: 0.6519 (t80)
REVERT: A  108 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5722 (t80)
REVERT: A  147 SER cc_start: 0.8547 (m) cc_final: 0.8098 (p)
REVERT: A  155 GLU cc_start: 0.7537 (pp20) cc_final: 0.7315 (pt0)
  outliers start: 19
  outliers final: 11
  residues processed: 155
  average time/residue: 0.2066
  time to fit residues: 42.2675
Evaluate side-chains
  129 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  253 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0770
   chunk 48 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.9740

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
A  18 ASN
A  50 ASN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.135155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.118152 restraints weight = 9517.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.121940 restraints weight = 5149.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.124580 restraints weight = 3331.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6928  Z= 0.178
  Angle     :  0.579   7.261   9409  Z= 0.291
  Chirality :  0.044   0.138   1028
  Planarity :  0.004   0.036   1221
  Dihedral  : 10.377 173.676    974
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.23 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.28), residues: 848
  helix: -0.30 (0.26), residues: 377
  sheet: -2.43 (0.48), residues: 108
  loop : -1.19 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.026   0.002   PHE B  20 
 TYR   0.010   0.001   TYR A 399 
 ARG   0.003   0.000   ARG A  84 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8610 (mpp) cc_final: 0.7910 (mpp)
REVERT: B   77 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7981 (mtt-85)
REVERT: B   86 ARG cc_start: 0.7015 (mmp-170) cc_final: 0.5217 (tpt170)
REVERT: B  118 ASP cc_start: 0.7395 (m-30) cc_final: 0.7093 (m-30)
REVERT: B  131 GLN cc_start: 0.6796 (tp40) cc_final: 0.6436 (tp40)
REVERT: B  300 MET cc_start: 0.8582 (ptp) cc_final: 0.8355 (ptp)
REVERT: B  406 MET cc_start: 0.7589 (tpp) cc_final: 0.7095 (ptm)
REVERT: A   56 THR cc_start: 0.8303 (m) cc_final: 0.7834 (p)
REVERT: A  103 TYR cc_start: 0.7095 (t80) cc_final: 0.6568 (t80)
REVERT: A  108 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5428 (t80)
REVERT: A  147 SER cc_start: 0.8483 (m) cc_final: 0.7984 (p)
REVERT: A  155 GLU cc_start: 0.7430 (pp20) cc_final: 0.7223 (pt0)
  outliers start: 27
  outliers final: 17
  residues processed: 158
  average time/residue: 0.2107
  time to fit residues: 44.5332
Evaluate side-chains
  141 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  275 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 GLN
B 298 ASN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.126895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.109001 restraints weight = 9635.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.112710 restraints weight = 5322.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.115293 restraints weight = 3525.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6928  Z= 0.284
  Angle     :  0.652  11.104   9409  Z= 0.326
  Chirality :  0.046   0.136   1028
  Planarity :  0.004   0.039   1221
  Dihedral  : 10.525 176.283    974
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 16.60 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.28), residues: 848
  helix: -0.38 (0.25), residues: 386
  sheet: -2.43 (0.47), residues: 110
  loop : -1.20 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A  28 
 PHE   0.025   0.002   PHE B  20 
 TYR   0.013   0.001   TYR A 282 
 ARG   0.005   0.001   ARG A 422 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8758 (mpp) cc_final: 0.7958 (mpp)
REVERT: B   86 ARG cc_start: 0.7122 (mmp-170) cc_final: 0.5469 (tpt170)
REVERT: B  118 ASP cc_start: 0.7400 (m-30) cc_final: 0.7176 (m-30)
REVERT: B  190 HIS cc_start: 0.8466 (t70) cc_final: 0.8217 (t-90)
REVERT: B  213 ARG cc_start: 0.8116 (ptp-110) cc_final: 0.7880 (ptp-110)
REVERT: B  245 GLN cc_start: 0.8475 (mt0) cc_final: 0.8241 (mt0)
REVERT: B  406 MET cc_start: 0.7889 (tpp) cc_final: 0.7004 (tpp)
REVERT: A  103 TYR cc_start: 0.7290 (t80) cc_final: 0.6775 (t80)
REVERT: A  108 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5353 (t80)
REVERT: A  147 SER cc_start: 0.8453 (m) cc_final: 0.8201 (p)
REVERT: A  155 GLU cc_start: 0.7549 (pp20) cc_final: 0.7259 (pt0)
REVERT: A  212 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8227 (mt)
REVERT: A  269 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8207 (pt)
REVERT: A  284 GLU cc_start: 0.7749 (tp30) cc_final: 0.7503 (tp30)
  outliers start: 35
  outliers final: 22
  residues processed: 161
  average time/residue: 0.2002
  time to fit residues: 42.2967
Evaluate side-chains
  146 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  354 CYS
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  367 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 GLN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.128381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.110415 restraints weight = 9667.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.114220 restraints weight = 5256.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.116887 restraints weight = 3441.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.5322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6928  Z= 0.203
  Angle     :  0.608   6.647   9409  Z= 0.305
  Chirality :  0.044   0.149   1028
  Planarity :  0.004   0.047   1221
  Dihedral  : 10.184 167.461    974
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 18.11 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.28), residues: 848
  helix: -0.26 (0.26), residues: 387
  sheet: -2.13 (0.49), residues: 110
  loop : -1.09 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  21 
 HIS   0.005   0.001   HIS B   6 
 PHE   0.033   0.002   PHE B  20 
 TYR   0.009   0.001   TYR A 282 
 ARG   0.009   0.000   ARG A 215 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.7282 (mmm) cc_final: 0.7075 (mmm)
REVERT: B   73 MET cc_start: 0.8807 (mpp) cc_final: 0.7858 (mpp)
REVERT: B   86 ARG cc_start: 0.7136 (mmp-170) cc_final: 0.5580 (tpt170)
REVERT: B  118 ASP cc_start: 0.7499 (m-30) cc_final: 0.7271 (m-30)
REVERT: B  190 HIS cc_start: 0.8474 (t70) cc_final: 0.8177 (t-90)
REVERT: B  213 ARG cc_start: 0.8123 (ptp-110) cc_final: 0.7822 (ptp-110)
REVERT: B  245 GLN cc_start: 0.8419 (mt0) cc_final: 0.8173 (mt0)
REVERT: B  299 MET cc_start: 0.6620 (pp-130) cc_final: 0.6387 (pp-130)
REVERT: B  329 GLN cc_start: 0.5637 (OUTLIER) cc_final: 0.5217 (tp40)
REVERT: B  406 MET cc_start: 0.7909 (tpp) cc_final: 0.7579 (tpp)
REVERT: A   56 THR cc_start: 0.8214 (m) cc_final: 0.7770 (p)
REVERT: A  103 TYR cc_start: 0.7207 (t80) cc_final: 0.6740 (t80)
REVERT: A  108 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5365 (t80)
REVERT: A  147 SER cc_start: 0.8380 (m) cc_final: 0.8091 (p)
REVERT: A  155 GLU cc_start: 0.7488 (pp20) cc_final: 0.7267 (pt0)
REVERT: A  202 PHE cc_start: 0.7049 (m-10) cc_final: 0.6758 (m-10)
REVERT: A  212 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8157 (mt)
REVERT: A  269 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8126 (pt)
REVERT: A  284 GLU cc_start: 0.7700 (tp30) cc_final: 0.7494 (tp30)
  outliers start: 32
  outliers final: 23
  residues processed: 167
  average time/residue: 0.1917
  time to fit residues: 42.7401
Evaluate side-chains
  150 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   83 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  329 GLN
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 21 optimal weight:    0.4980
   chunk 50 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 HIS
B 329 GLN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.129775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.112215 restraints weight = 9520.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.116001 restraints weight = 5163.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.118653 restraints weight = 3376.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6928  Z= 0.179
  Angle     :  0.608   6.833   9409  Z= 0.305
  Chirality :  0.044   0.144   1028
  Planarity :  0.004   0.043   1221
  Dihedral  : 10.059 164.107    974
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.44 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.28), residues: 848
  helix: -0.14 (0.26), residues: 384
  sheet: -2.00 (0.49), residues: 110
  loop : -1.05 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 307 
 PHE   0.032   0.002   PHE B  20 
 TYR   0.007   0.001   TYR A 399 
 ARG   0.008   0.001   ARG A 215 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8829 (mpp) cc_final: 0.7797 (mpp)
REVERT: B   86 ARG cc_start: 0.7068 (mmp-170) cc_final: 0.5583 (tpt170)
REVERT: B  118 ASP cc_start: 0.7480 (m-30) cc_final: 0.7238 (m-30)
REVERT: B  213 ARG cc_start: 0.8082 (ptp-110) cc_final: 0.7767 (ptp-110)
REVERT: B  245 GLN cc_start: 0.8400 (mt0) cc_final: 0.8076 (mt0)
REVERT: B  329 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.5017 (tp40)
REVERT: B  406 MET cc_start: 0.7842 (tpp) cc_final: 0.7593 (tpp)
REVERT: A   56 THR cc_start: 0.8224 (m) cc_final: 0.7961 (p)
REVERT: A  103 TYR cc_start: 0.7256 (t80) cc_final: 0.6833 (t80)
REVERT: A  108 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.5379 (t80)
REVERT: A  147 SER cc_start: 0.8359 (m) cc_final: 0.8069 (p)
REVERT: A  203 MET cc_start: 0.8254 (mmm) cc_final: 0.7740 (mmm)
REVERT: A  212 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8149 (mt)
REVERT: A  269 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7979 (pt)
REVERT: A  284 GLU cc_start: 0.7672 (tp30) cc_final: 0.7466 (tp30)
  outliers start: 27
  outliers final: 21
  residues processed: 158
  average time/residue: 0.1935
  time to fit residues: 40.5191
Evaluate side-chains
  144 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  329 GLN
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  422 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.130078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.112924 restraints weight = 9619.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.116687 restraints weight = 5210.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.119273 restraints weight = 3390.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.5687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6928  Z= 0.203
  Angle     :  0.625   7.993   9409  Z= 0.312
  Chirality :  0.044   0.148   1028
  Planarity :  0.004   0.037   1221
  Dihedral  : 10.027 161.509    974
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 19.75 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.29), residues: 848
  helix:  0.09 (0.27), residues: 371
  sheet: -1.83 (0.51), residues: 107
  loop : -0.89 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 307 
 PHE   0.030   0.002   PHE B  20 
 TYR   0.010   0.001   TYR B 200 
 ARG   0.007   0.001   ARG A 215 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8884 (mpp) cc_final: 0.7708 (mpp)
REVERT: B   86 ARG cc_start: 0.7013 (mmp-170) cc_final: 0.5612 (tpt170)
REVERT: B  190 HIS cc_start: 0.8429 (t70) cc_final: 0.8134 (t-90)
REVERT: B  213 ARG cc_start: 0.8083 (ptp-110) cc_final: 0.7758 (ptp-110)
REVERT: B  406 MET cc_start: 0.7898 (tpp) cc_final: 0.7245 (tpp)
REVERT: A   56 THR cc_start: 0.8220 (m) cc_final: 0.7967 (p)
REVERT: A  103 TYR cc_start: 0.7303 (t80) cc_final: 0.6857 (t80)
REVERT: A  108 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.5289 (t80)
REVERT: A  147 SER cc_start: 0.8424 (m) cc_final: 0.8094 (p)
REVERT: A  212 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8145 (mt)
  outliers start: 34
  outliers final: 28
  residues processed: 153
  average time/residue: 0.1910
  time to fit residues: 38.6212
Evaluate side-chains
  149 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue   83 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  422 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0470
   chunk 47 optimal weight:    0.0970
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.3490

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
A  61 HIS
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** 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 = 0.3916 r_free = 0.3916 target = 0.134696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.117798 restraints weight = 9488.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.121548 restraints weight = 5089.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.124156 restraints weight = 3286.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.5820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6928  Z= 0.165
  Angle     :  0.615   7.048   9409  Z= 0.309
  Chirality :  0.044   0.157   1028
  Planarity :  0.004   0.036   1221
  Dihedral  :  9.871 157.404    974
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.95 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.29), residues: 848
  helix:  0.11 (0.27), residues: 371
  sheet: -1.49 (0.55), residues: 99
  loop : -0.98 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 307 
 PHE   0.050   0.002   PHE B  20 
 TYR   0.013   0.001   TYR B 340 
 ARG   0.007   0.001   ARG A 215 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8893 (mpp) cc_final: 0.7734 (mpp)
REVERT: B   86 ARG cc_start: 0.6768 (mmp-170) cc_final: 0.5295 (tpt170)
REVERT: B  203 ASP cc_start: 0.7320 (t0) cc_final: 0.6769 (p0)
REVERT: B  213 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7686 (ptp-110)
REVERT: B  276 ARG cc_start: 0.7087 (mmm160) cc_final: 0.6873 (mmm160)
REVERT: B  306 ARG cc_start: 0.7796 (mpt90) cc_final: 0.7443 (mtt90)
REVERT: B  406 MET cc_start: 0.7694 (tpp) cc_final: 0.7086 (tpp)
REVERT: A  103 TYR cc_start: 0.7306 (t80) cc_final: 0.6973 (t80)
REVERT: A  108 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.5262 (t80)
REVERT: A  110 ILE cc_start: 0.8520 (mm) cc_final: 0.8180 (mp)
REVERT: A  147 SER cc_start: 0.8391 (m) cc_final: 0.7970 (p)
REVERT: A  212 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8087 (mt)
  outliers start: 21
  outliers final: 16
  residues processed: 148
  average time/residue: 0.2370
  time to fit residues: 46.7020
Evaluate side-chains
  142 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    0.0170
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0670
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   overall best weight:    0.8358

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

Flipped N/Q/H residues before XYZ refinement:
B  57 HIS
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 GLN
** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.133860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.116308 restraints weight = 9698.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.120113 restraints weight = 5202.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.122785 restraints weight = 3381.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.5926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6928  Z= 0.199
  Angle     :  0.638   8.942   9409  Z= 0.320
  Chirality :  0.044   0.154   1028
  Planarity :  0.004   0.035   1221
  Dihedral  :  9.820 153.732    974
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.85 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.29), residues: 848
  helix:  0.11 (0.27), residues: 370
  sheet: -1.55 (0.54), residues: 99
  loop : -0.96 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A   8 
 PHE   0.050   0.002   PHE B  20 
 TYR   0.017   0.001   TYR B 340 
 ARG   0.006   0.001   ARG A 215 

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

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

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1696 Ramachandran restraints generated.
    848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8930 (mpp) cc_final: 0.7752 (mpp)
REVERT: B   86 ARG cc_start: 0.6612 (mmp-170) cc_final: 0.5223 (tpt170)
REVERT: B  190 HIS cc_start: 0.8456 (t70) cc_final: 0.8194 (t-90)
REVERT: B  276 ARG cc_start: 0.7213 (mmm160) cc_final: 0.6962 (mmm160)
REVERT: B  406 MET cc_start: 0.7707 (tpp) cc_final: 0.7086 (tpp)
REVERT: A  103 TYR cc_start: 0.7356 (t80) cc_final: 0.6980 (t80)
REVERT: A  147 SER cc_start: 0.8439 (m) cc_final: 0.7995 (p)
REVERT: A  212 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8090 (mt)
REVERT: A  255 PHE cc_start: 0.8681 (t80) cc_final: 0.8243 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 147
  average time/residue: 0.2046
  time to fit residues: 39.7715
Evaluate side-chains
  148 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  127 CYS
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  422 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 47 optimal weight:    0.1980
   chunk 15 optimal weight:    7.9990
   chunk 75 optimal weight:    0.0870
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0770
   chunk 12 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.2516

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.136473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.118476 restraints weight = 9535.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.122344 restraints weight = 5153.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.125096 restraints weight = 3355.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.6094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6928  Z= 0.167
  Angle     :  0.621   8.804   9409  Z= 0.309
  Chirality :  0.044   0.156   1028
  Planarity :  0.004   0.036   1221
  Dihedral  :  9.815 149.323    974
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.54 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.29), residues: 848
  helix:  0.16 (0.27), residues: 369
  sheet: -1.56 (0.54), residues: 98
  loop : -0.93 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A   8 
 PHE   0.040   0.002   PHE B  20 
 TYR   0.018   0.001   TYR B 200 
 ARG   0.006   0.001   ARG A 215 

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Job complete
usr+sys time: 2748.18 seconds
wall clock time: 50 minutes 12.83 seconds (3012.83 seconds total)