Starting phenix.real_space_refine
on Fri Aug 22 18:28:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e7b_8997/08_2025/6e7b_8997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e7b_8997/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e7b_8997/08_2025/6e7b_8997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e7b_8997/08_2025/6e7b_8997.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e7b_8997/08_2025/6e7b_8997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e7b_8997/08_2025/6e7b_8997.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.52, per 1000 atoms: 0.22
  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: 0.59
  Conformation dependent library (CDL) restraints added in 309.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.14
  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: 0.93

  Time building geometry restraints manager: 0.75 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:             9.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.030
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.110
-------------------------------------------------------------------------------
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= 0.274
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG B 241 
 TYR   0.013   0.002   TYR B 208 
 PHE   0.019   0.002   PHE B 212 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.008   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 6928)
  covalent geometry    : angle       0.82842 ( 9409)
  hydrogen bonds       : bond        0.28612 (  278)
  hydrogen bonds       : angle      10.12227 (  828)

*********************** 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  : 0.286 
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: 0.7744 (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: 0.7314 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 224
  average time/residue: 0.1079
  time to fit residues: 30.3025
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  : 0.247 
-------------------------------------------------------------------------------
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 49 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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 206 ASN
A 300 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.129679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.112066 restraints weight = 9836.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.115936 restraints weight = 5330.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.118639 restraints weight = 3467.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.120428 restraints weight = 2498.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.121832 restraints weight = 1959.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6928  Z= 0.256
  Angle     :  0.744   6.949   9409  Z= 0.382
  Chirality :  0.050   0.169   1028
  Planarity :  0.005   0.056   1221
  Dihedral  : 11.005 161.481    976
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.07 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.73 (0.26), residues: 848
  helix: -1.44 (0.23), residues: 363
  sheet: -3.35 (0.44), residues: 93
  loop : -1.62 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  84 
 TYR   0.016   0.002   TYR B  36 
 PHE   0.028   0.003   PHE A 255 
 TRP   0.020   0.002   TRP A  21 
 HIS   0.008   0.002   HIS A  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 6928)
  covalent geometry    : angle       0.74357 ( 9409)
  hydrogen bonds       : bond        0.05464 (  278)
  hydrogen bonds       : angle       5.85896 (  828)

*********************** 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
  167 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: B   86 ARG cc_start: 0.7062 (mmp-170) cc_final: 0.6412 (tpm170)
REVERT: A  103 TYR cc_start: 0.7014 (t80) cc_final: 0.6559 (t80)
REVERT: A  108 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5963 (t80)
REVERT: A  147 SER cc_start: 0.8663 (m) cc_final: 0.8254 (p)
REVERT: A  276 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8309 (pt)
  outliers start: 20
  outliers final: 10
  residues processed: 162
  average time/residue: 0.0810
  time to fit residues: 17.4417
Evaluate side-chains
  127 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  130 THR
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  276 ILE
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 80 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
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**

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 = 0.134648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.118268 restraints weight = 9490.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.122067 restraints weight = 5095.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.124718 restraints weight = 3260.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.126580 restraints weight = 2317.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.127782 restraints weight = 1765.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.4379

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= 0.132
  Angle     :  0.611   7.409   9409  Z= 0.312
  Chirality :  0.045   0.143   1028
  Planarity :  0.004   0.035   1221
  Dihedral  : 10.654 171.098    974
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.40 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.27), residues: 848
  helix: -0.67 (0.25), residues: 373
  sheet: -2.63 (0.48), residues: 104
  loop : -1.47 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  84 
 TYR   0.011   0.001   TYR A 399 
 PHE   0.033   0.002   PHE B  20 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6928)
  covalent geometry    : angle       0.61075 ( 9409)
  hydrogen bonds       : bond        0.04479 (  278)
  hydrogen bonds       : angle       5.26088 (  828)

*********************** 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
  165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8516 (mpp) cc_final: 0.7968 (mpp)
REVERT: A  108 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5784 (t80)
REVERT: A  147 SER cc_start: 0.8528 (m) cc_final: 0.8100 (p)
REVERT: A  225 THR cc_start: 0.8825 (p) cc_final: 0.8623 (t)
REVERT: A  234 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8168 (mt)
  outliers start: 17
  outliers final: 11
  residues processed: 162
  average time/residue: 0.0959
  time to fit residues: 20.2000
Evaluate side-chains
  126 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
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    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  192 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  234 ILE
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 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 42 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A  18 ASN
** A  61 HIS ** 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 258 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.130625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.113005 restraints weight = 9697.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.116857 restraints weight = 5227.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.119569 restraints weight = 3382.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.121482 restraints weight = 2440.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.122837 restraints weight = 1887.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4844

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= 0.146
  Angle     :  0.609   8.148   9409  Z= 0.308
  Chirality :  0.045   0.151   1028
  Planarity :  0.004   0.037   1221
  Dihedral  : 10.565 178.058    974
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.78 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.28), residues: 848
  helix: -0.33 (0.26), residues: 374
  sheet: -2.46 (0.47), residues: 110
  loop : -1.24 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  84 
 TYR   0.013   0.001   TYR A 357 
 PHE   0.031   0.002   PHE B  20 
 TRP   0.015   0.002   TRP A  21 
 HIS   0.003   0.001   HIS B 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6928)
  covalent geometry    : angle       0.60853 ( 9409)
  hydrogen bonds       : bond        0.04188 (  278)
  hydrogen bonds       : angle       5.02827 (  828)

*********************** 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
  158 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8572 (mpp) cc_final: 0.7978 (mpp)
REVERT: B  207 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8071 (mm)
REVERT: B  267 MET cc_start: 0.8207 (mtm) cc_final: 0.7986 (mtp)
REVERT: A   56 THR cc_start: 0.8203 (m) cc_final: 0.7693 (p)
REVERT: A  103 TYR cc_start: 0.7164 (t80) cc_final: 0.6530 (t80)
REVERT: A  108 TYR cc_start: 0.6095 (OUTLIER) cc_final: 0.5490 (t80)
REVERT: A  147 SER cc_start: 0.8417 (m) cc_final: 0.8007 (p)
  outliers start: 30
  outliers final: 19
  residues processed: 150
  average time/residue: 0.0802
  time to fit residues: 16.3523
Evaluate side-chains
  133 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  207 LEU
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  161 TYR
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  234 ILE
Chi-restraints excluded: chain A residue  238 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  275 VAL
Chi-restraints excluded: chain A residue  378 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 70 optimal weight:    0.3980
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 245 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 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.131144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.113684 restraints weight = 9605.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117549 restraints weight = 5145.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.120244 restraints weight = 3307.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.122139 restraints weight = 2382.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.123376 restraints weight = 1836.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6928  Z= 0.129
  Angle     :  0.582   8.279   9409  Z= 0.293
  Chirality :  0.044   0.145   1028
  Planarity :  0.004   0.035   1221
  Dihedral  : 10.245 172.334    974
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.01 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.28), residues: 848
  helix: -0.14 (0.26), residues: 375
  sheet: -2.29 (0.48), residues: 110
  loop : -1.14 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 359 
 TYR   0.008   0.001   TYR A 399 
 PHE   0.020   0.002   PHE B 385 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6928)
  covalent geometry    : angle       0.58180 ( 9409)
  hydrogen bonds       : bond        0.03939 (  278)
  hydrogen bonds       : angle       4.86148 (  828)

*********************** 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
  154 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.8654 (mpp) cc_final: 0.7847 (mpp)
REVERT: B  213 ARG cc_start: 0.8078 (ptp-110) cc_final: 0.7836 (ptp-110)
REVERT: B  267 MET cc_start: 0.8207 (mtm) cc_final: 0.7943 (mtp)
REVERT: B  406 MET cc_start: 0.7730 (tpp) cc_final: 0.7204 (ptm)
REVERT: A   56 THR cc_start: 0.8233 (m) cc_final: 0.7831 (p)
REVERT: A  108 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5339 (t80)
REVERT: A  147 SER cc_start: 0.8419 (m) cc_final: 0.8082 (p)
REVERT: A  212 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8038 (mt)
REVERT: A  269 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8146 (pt)
  outliers start: 27
  outliers final: 19
  residues processed: 148
  average time/residue: 0.0859
  time to fit residues: 17.2352
Evaluate side-chains
  135 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  351 VAL
Chi-restraints excluded: chain B residue  368 ILE
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  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  192 HIS
Chi-restraints excluded: chain A residue  212 ILE
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    2.1186

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.127729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.111133 restraints weight = 9745.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.114734 restraints weight = 5261.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.117238 restraints weight = 3418.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119036 restraints weight = 2471.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.120190 restraints weight = 1913.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.5466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6928  Z= 0.172
  Angle     :  0.628   9.346   9409  Z= 0.317
  Chirality :  0.046   0.163   1028
  Planarity :  0.004   0.037   1221
  Dihedral  : 10.243 167.856    974
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 17.97 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.28), residues: 848
  helix: -0.13 (0.26), residues: 380
  sheet: -2.24 (0.48), residues: 110
  loop : -1.07 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 276 
 TYR   0.009   0.001   TYR A 408 
 PHE   0.021   0.002   PHE B 385 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.004   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6928)
  covalent geometry    : angle       0.62807 ( 9409)
  hydrogen bonds       : bond        0.04074 (  278)
  hydrogen bonds       : angle       4.89441 (  828)

*********************** 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
  156 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 HIS cc_start: 0.5865 (t-90) cc_final: 0.5648 (t-90)
REVERT: B   73 MET cc_start: 0.8767 (mpp) cc_final: 0.8022 (mpp)
REVERT: B  213 ARG cc_start: 0.8109 (ptp-110) cc_final: 0.7834 (ptp-110)
REVERT: B  267 MET cc_start: 0.8345 (mtm) cc_final: 0.8063 (mtp)
REVERT: B  276 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7058 (mmm160)
REVERT: B  406 MET cc_start: 0.7932 (tpp) cc_final: 0.6986 (tpp)
REVERT: A   56 THR cc_start: 0.8234 (m) cc_final: 0.7762 (p)
REVERT: A  103 TYR cc_start: 0.7237 (t80) cc_final: 0.6719 (t80)
REVERT: A  108 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5281 (t80)
REVERT: A  147 SER cc_start: 0.8403 (m) cc_final: 0.8201 (p)
REVERT: A  199 ASP cc_start: 0.7049 (m-30) cc_final: 0.6743 (m-30)
REVERT: A  212 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8175 (mt)
REVERT: A  269 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8133 (pt)
  outliers start: 30
  outliers final: 21
  residues processed: 149
  average time/residue: 0.0848
  time to fit residues: 16.9911
Evaluate side-chains
  143 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  145 SER
Chi-restraints excluded: chain B residue  155 VAL
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    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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0383 > 50:
  distance: 18 - 20:  34.308
  distance: 20 - 21:  57.029
  distance: 21 - 24:  39.051
  distance: 22 - 23:  39.888
  distance: 22 - 28:  31.821
  distance: 24 - 25:  39.856
  distance: 24 - 26:  38.780
  distance: 25 - 27:  70.201
  distance: 28 - 29:   8.364
  distance: 29 - 32:  40.410
  distance: 30 - 37:  40.303
  distance: 33 - 34:  11.271
  distance: 34 - 35:  30.458
  distance: 34 - 36:  11.469
  distance: 37 - 38:  40.725
  distance: 38 - 39:  38.298
  distance: 38 - 41:  40.921
  distance: 39 - 40:  40.553
  distance: 41 - 42:  41.116
  distance: 42 - 43:  39.129
  distance: 46 - 47:  39.694
  distance: 46 - 52:  40.173
  distance: 48 - 49:  39.847
  distance: 54 - 55:  40.821
  distance: 54 - 56:  39.199
  distance: 56 - 57:  57.030
  distance: 57 - 60:  36.677
  distance: 58 - 59:  39.385
  distance: 58 - 65:  38.834
  distance: 60 - 61:  56.329
  distance: 61 - 62:  67.883
  distance: 62 - 63:   3.609
  distance: 65 - 66:  56.119
  distance: 66 - 67:  57.839
  distance: 66 - 69:  67.218
  distance: 67 - 68:  40.889
  distance: 69 - 70:  38.912
  distance: 71 - 72:  41.737
  distance: 73 - 74:  39.651
  distance: 73 - 79:  39.355
  distance: 74 - 75:  40.145
  distance: 75 - 76:  40.656
  distance: 77 - 78:  55.977
  distance: 80 - 81:   9.532
  distance: 81 - 82:   9.934
  distance: 81 - 84:   5.228
  distance: 82 - 83:   9.582
  distance: 82 - 88:   8.636
  distance: 83 - 105:  14.004
  distance: 84 - 85:   6.444
  distance: 85 - 86:   8.187
  distance: 85 - 87:   5.522
  distance: 88 - 89:   6.865
  distance: 89 - 90:   5.536
  distance: 89 - 92:   7.378
  distance: 90 - 91:   4.393
  distance: 90 - 94:   5.546
  distance: 91 - 111:   8.084
  distance: 92 - 93:  18.093