Starting phenix.real_space_refine
on Fri Aug 22 19:40:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p9v_13267/08_2025/7p9v_13267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p9v_13267/08_2025/7p9v_13267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p9v_13267/08_2025/7p9v_13267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p9v_13267/08_2025/7p9v_13267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p9v_13267/08_2025/7p9v_13267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p9v_13267/08_2025/7p9v_13267.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.046
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4751      2.51       5
     N    1185      2.21       5
     O    1323      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 7286
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3616
          Classifications: {'peptide': 464}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441}
    Chain: "B"
      Number of atoms: 3558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3558
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 23, 'TRANS': 431}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.15, per 1000 atoms: 0.30
  Number of scatterers: 7286
  At special positions: 0
  Unit cell: (85.696, 79.872, 131.456, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1323      8.00
     N    1185      7.00
     C    4751      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 158 " distance=2.21

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 411.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      57.5% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 179 through 208
      removed outlier: 3.574A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
    Processing helix  chain 'A' and resid 242 through 247
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 283 through 286
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.704A  pdb=" N   SER A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 342
      removed outlier: 4.336A  pdb=" N   LYS A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.746A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 414 through 427
      removed outlier: 4.261A  pdb=" N   VAL A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   THR A 427 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.650A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 515
      removed outlier: 3.811A  pdb=" N   GLU A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 534 through 540
      removed outlier: 3.624A  pdb=" N   LEU A 538 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   HIS A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 4.006A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 58
      removed outlier: 3.809A  pdb=" N   THR B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B  58 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 72
      Proline residue:  B  66  - end of helix
      removed outlier: 3.602A  pdb=" N   ASN B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 105
      removed outlier: 3.653A  pdb=" N   ILE B  82 " --> pdb=" O   MET B  78 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LYS B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
      removed outlier: 3.899A  pdb=" N   GLU B 116 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 133
      removed outlier: 3.618A  pdb=" N   ALA B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 152
      removed outlier: 3.579A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 3.536A  pdb=" N   ILE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS B 166 " --> pdb=" O   GLU B 162 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 211
      removed outlier: 3.927A  pdb=" N   ILE B 190 " --> pdb=" O   TRP B 186 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLN B 191 " --> pdb=" O   SER B 187 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B 202 " --> pdb=" O   LYS B 198 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ILE B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL B 207 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 231 through 233
      No H-bonds generated for 'chain 'B' and resid 231 through 233'
    Processing helix  chain 'B' and resid 234 through 246
      removed outlier: 3.739A  pdb=" N   ALA B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   TYR B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 292
      removed outlier: 4.365A  pdb=" N   ILE B 276 " --> pdb=" O   ILE B 272 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 302 through 312
      removed outlier: 3.772A  pdb=" N   THR B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.589A  pdb=" N   ALA B 318 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      Proline residue:  B 320  - end of helix
      removed outlier: 4.944A  pdb=" N   ALA B 324 " --> pdb=" O   PRO B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 335
      No H-bonds generated for 'chain 'B' and resid 333 through 335'
    Processing helix  chain 'B' and resid 336 through 348
      removed outlier: 3.985A  pdb=" N   LEU B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLU B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 355
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.536A  pdb=" N   VAL B 369 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE B 370 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 370'
    Processing helix  chain 'B' and resid 371 through 382
      removed outlier: 4.265A  pdb=" N   LEU B 375 " --> pdb=" O   VAL B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 402
      removed outlier: 4.271A  pdb=" N   ASN B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B 399 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 411
      removed outlier: 3.858A  pdb=" N   LEU B 407 " --> pdb=" O   ALA B 403 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR B 409 " --> pdb=" O   ALA B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 439
      removed outlier: 5.537A  pdb=" N   PHE B 433 " --> pdb=" O   ALA B 429 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   PHE B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 443
      removed outlier: 3.786A  pdb=" N   LEU B 443 " --> pdb=" O   ALA B 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 440 through 443'
    Processing helix  chain 'B' and resid 450 through 460
    Processing helix  chain 'B' and resid 461 through 466
      removed outlier: 3.582A  pdb=" N   TYR B 464 " --> pdb=" O   VAL B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 7.316A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 8.752A  pdb=" N   GLY A 380 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 8.637A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268
      removed outlier: 6.171A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 3.567A  pdb=" N   PHE A 545 " --> pdb=" O   SER A 553 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 611
      removed outlier: 7.052A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 359

    318 hydrogen bonds defined for protein.
    924 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: 1.09

  Time building geometry restraints manager: 0.88 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: 2252
        1.34 -     1.46: 1535
        1.46 -     1.58: 3631
        1.58 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 7463
  Sorted by residual:
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.456 -0.050 2.00e-02 2.50e+03 6.38e+00
  bond pdb=" CA  LEU A 335 "
       pdb=" C   LEU A 335 "
    ideal  model  delta    sigma   weight residual
    1.522  1.492  0.030 1.43e-02 4.89e+03 4.44e+00
  bond pdb=" C   LEU A 335 "
       pdb=" N   GLU A 336 "
    ideal  model  delta    sigma   weight residual
    1.332  1.310  0.022 1.29e-02 6.01e+03 2.96e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.66e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.52e+00
  ... (remaining 7458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 9909
        2.20 -     4.40: 209
        4.40 -     6.59: 24
        6.59 -     8.79: 6
        8.79 -    10.99: 3
  Bond angle restraints: 10151
  Sorted by residual:
  angle pdb=" N   ILE B 205 "
        pdb=" CA  ILE B 205 "
        pdb=" C   ILE B 205 "
      ideal   model   delta    sigma   weight residual
     111.90  109.22    2.68 8.10e-01 1.52e+00 1.10e+01
  angle pdb=" N   GLY B 334 "
        pdb=" CA  GLY B 334 "
        pdb=" C   GLY B 334 "
      ideal   model   delta    sigma   weight residual
     115.66  110.27    5.39 1.63e+00 3.76e-01 1.10e+01
  angle pdb=" N   LEU B 430 "
        pdb=" CA  LEU B 430 "
        pdb=" C   LEU B 430 "
      ideal   model   delta    sigma   weight residual
     114.75  110.66    4.09 1.26e+00 6.30e-01 1.05e+01
  angle pdb=" N   VAL B  76 "
        pdb=" CA  VAL B  76 "
        pdb=" C   VAL B  76 "
      ideal   model   delta    sigma   weight residual
     111.56  108.80    2.76 8.60e-01 1.35e+00 1.03e+01
  angle pdb=" CA  TRP B 476 "
        pdb=" CB  TRP B 476 "
        pdb=" CG  TRP B 476 "
      ideal   model   delta    sigma   weight residual
     113.60  107.53    6.07 1.90e+00 2.77e-01 1.02e+01
  ... (remaining 10146 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.89: 4167
       21.89 -    43.78: 280
       43.78 -    65.66: 29
       65.66 -    87.55: 11
       87.55 -   109.44: 9
  Dihedral angle restraints: 4496
    sinusoidal: 1857
      harmonic: 2639
  Sorted by residual:
  dihedral pdb=" CA  PRO B 320 "
           pdb=" C   PRO B 320 "
           pdb=" N   ILE B 321 "
           pdb=" CA  ILE B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.09   21.91     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  LYS A 270 "
           pdb=" C   LYS A 270 "
           pdb=" N   ASP A 271 "
           pdb=" CA  ASP A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  ALA B 429 "
           pdb=" C   ALA B 429 "
           pdb=" N   LEU B 430 "
           pdb=" CA  LEU B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.75   20.25     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4493 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1125
       0.092 -    0.185: 67
       0.185 -    0.277: 2
       0.277 -    0.369: 0
       0.369 -    0.461: 1
  Chirality restraints: 1195
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.29   -0.20 2.00e-01 2.50e+01 9.91e-01
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.13e-01
  ... (remaining 1192 not shown)

  Planarity restraints: 1262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 476 "   -0.032 2.00e-02 2.50e+03   2.67e-02 1.78e+01
        pdb=" CG  TRP B 476 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 476 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 476 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 476 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 476 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 476 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 476 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 476 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 476 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 627 "   -0.060 5.00e-02 4.00e+02   9.29e-02 1.38e+01
        pdb=" N   PRO A 628 "    0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO A 628 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 628 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 321 "    0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   ILE B 321 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B 321 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE B 322 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1259 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 138
        2.66 -     3.22: 7319
        3.22 -     3.78: 11063
        3.78 -     4.34: 15376
        4.34 -     4.90: 25040
  Nonbonded interactions: 58936
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 446 "
            pdb=" OG  SER B 449 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" OH  TYR B 111 "
            pdb=" OE2 GLU B 348 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" OH  TYR A 469 "
            pdb=" O   PRO A 488 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" O   TRP A 492 "
            pdb=" NZ  LYS A 511 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG  SER B  75 "
            pdb=" O   ALA B 224 "
     model   vdw
     2.203 3.040
  ... (remaining 58931 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
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   0.182   7472  Z= 0.258
  Angle     :  0.894  27.903  10177  Z= 0.467
  Chirality :  0.048   0.461   1195
  Planarity :  0.005   0.093   1258
  Dihedral  : 15.249 109.438   2797
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -2.67 (0.27), residues: 915
  helix: -1.08 (0.24), residues: 461
  sheet: -2.92 (0.63), residues: 63
  loop : -2.34 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 563 
 TYR   0.015   0.002   TYR A 629 
 PHE   0.023   0.002   PHE A 291 
 TRP   0.072   0.003   TRP B 476 
 HIS   0.011   0.001   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 7463)
  covalent geometry    : angle       0.81890 (10151)
  SS BOND              : bond        0.18201 (    1)
  SS BOND              : angle      22.52824 (    2)
  hydrogen bonds       : bond        0.19373 (  318)
  hydrogen bonds       : angle       7.61254 (  924)
  link_BETA1-4         : bond        0.00543 (    4)
  link_BETA1-4         : angle       2.27726 (   12)
  link_NAG-ASN         : bond        0.00269 (    4)
  link_NAG-ASN         : angle       4.59765 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: B  476 TRP cc_start: 0.3558 (m100) cc_final: 0.2302 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0820
  time to fit residues: 18.4973
Evaluate side-chains
  125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0270
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN
B 110 HIS
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.154995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.138820 restraints weight = 11905.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.17
r_work: 0.3638 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7472  Z= 0.154
  Angle     :  0.740  12.082  10177  Z= 0.354
  Chirality :  0.046   0.314   1195
  Planarity :  0.005   0.055   1258
  Dihedral  : 10.863  89.101   1151
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.00 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -2.38 (0.27), residues: 915
  helix: -0.58 (0.23), residues: 478
  sheet: -2.78 (0.57), residues: 72
  loop : -2.62 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 148 
 TYR   0.029   0.002   TYR A 313 
 PHE   0.025   0.002   PHE A 524 
 TRP   0.022   0.001   TRP B 476 
 HIS   0.007   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7463)
  covalent geometry    : angle       0.72433 (10151)
  SS BOND              : bond        0.00523 (    1)
  SS BOND              : angle       1.11623 (    2)
  hydrogen bonds       : bond        0.04257 (  318)
  hydrogen bonds       : angle       5.13472 (  924)
  link_BETA1-4         : bond        0.00629 (    4)
  link_BETA1-4         : angle       2.35631 (   12)
  link_NAG-ASN         : bond        0.00410 (    4)
  link_NAG-ASN         : angle       3.85379 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.285 
Fit side-chains
REVERT: B  476 TRP cc_start: 0.4626 (m100) cc_final: 0.3421 (m100)
  outliers start: 11
  outliers final: 5
  residues processed: 152
  average time/residue: 0.0767
  time to fit residues: 16.5666
Evaluate side-chains
  134 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0870
   chunk 83 optimal weight:    0.0370
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.5636

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

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.156162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140269 restraints weight = 11768.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.15
r_work: 0.3653 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7472  Z= 0.132
  Angle     :  0.675  10.523  10177  Z= 0.322
  Chirality :  0.044   0.305   1195
  Planarity :  0.004   0.051   1258
  Dihedral  :  9.686  74.281   1151
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.47 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.93 (0.27), residues: 915
  helix: -0.21 (0.24), residues: 476
  sheet: -2.56 (0.63), residues: 64
  loop : -2.43 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 563 
 TYR   0.029   0.001   TYR A 313 
 PHE   0.025   0.001   PHE A 524 
 TRP   0.015   0.001   TRP B 476 
 HIS   0.005   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7463)
  covalent geometry    : angle       0.65851 (10151)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.41595 (    2)
  hydrogen bonds       : bond        0.03905 (  318)
  hydrogen bonds       : angle       4.78336 (  924)
  link_BETA1-4         : bond        0.00575 (    4)
  link_BETA1-4         : angle       2.37424 (   12)
  link_NAG-ASN         : bond        0.00376 (    4)
  link_NAG-ASN         : angle       3.72211 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  186 LEU cc_start: 0.8070 (mm) cc_final: 0.7804 (mp)
REVERT: A  485 MET cc_start: 0.7179 (ppp) cc_final: 0.6153 (tpt)
REVERT: B  416 ASP cc_start: 0.7128 (m-30) cc_final: 0.6863 (t0)
REVERT: B  476 TRP cc_start: 0.4513 (m100) cc_final: 0.3331 (m100)
REVERT: B  480 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6199 (ttm)
  outliers start: 18
  outliers final: 10
  residues processed: 155
  average time/residue: 0.0723
  time to fit residues: 16.2426
Evaluate side-chains
  140 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
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: 64.6975 > 50:
  distance: 2 - 18:   8.688
  distance: 6 - 26:   8.455
  distance: 13 - 34:  10.944
  distance: 16 - 18:   5.709
  distance: 17 - 39:  12.346
  distance: 18 - 19:  13.363
  distance: 19 - 20:  12.553
  distance: 19 - 22:  12.127
  distance: 20 - 21:   7.377
  distance: 20 - 26:  14.780
  distance: 21 - 43:  24.359
  distance: 22 - 23:  15.196
  distance: 23 - 24:  10.656
  distance: 24 - 25:  12.551
  distance: 26 - 27:  12.560
  distance: 27 - 28:  10.987
  distance: 27 - 30:   7.250
  distance: 28 - 29:   7.608
  distance: 28 - 34:   4.859
  distance: 29 - 48:  16.191
  distance: 30 - 31:  10.645
  distance: 31 - 32:  27.773
  distance: 31 - 33:  29.308
  distance: 34 - 35:  10.147
  distance: 35 - 36:  10.601
  distance: 35 - 38:   7.595
  distance: 36 - 37:  14.247
  distance: 36 - 39:   4.679
  distance: 37 - 55:  22.040
  distance: 39 - 40:   9.166
  distance: 40 - 41:   5.492
  distance: 41 - 42:  10.811
  distance: 41 - 43:  18.320
  distance: 42 - 62:  32.756
  distance: 43 - 44:  10.686
  distance: 44 - 45:  23.537
  distance: 44 - 47:  19.304
  distance: 45 - 46:   7.124
  distance: 45 - 48:  14.465
  distance: 46 - 70:  12.661
  distance: 48 - 49:  15.594
  distance: 49 - 50:   8.923
  distance: 49 - 52:   4.887
  distance: 50 - 51:   7.564
  distance: 50 - 55:   6.256
  distance: 51 - 78:  35.116
  distance: 52 - 53:   4.878
  distance: 52 - 54:   6.742
  distance: 55 - 56:  13.376
  distance: 56 - 57:   5.563
  distance: 56 - 59:  16.800
  distance: 57 - 58:   9.246
  distance: 58 - 85:  26.379
  distance: 59 - 60:  13.319
  distance: 59 - 61:  10.447
  distance: 62 - 63:   3.053
  distance: 63 - 66:  14.553
  distance: 64 - 70:  19.338
  distance: 65 - 92:  34.790
  distance: 66 - 67:  23.362
  distance: 66 - 68:  15.623
  distance: 67 - 69:   4.408
  distance: 70 - 71:  11.641
  distance: 71 - 72:  10.956
  distance: 71 - 74:   9.850
  distance: 72 - 73:  16.894
  distance: 72 - 78:  40.008
  distance: 74 - 75:  13.523
  distance: 74 - 76:  23.146
  distance: 75 - 77:  11.100
  distance: 78 - 79:  36.247
  distance: 79 - 80:  10.754
  distance: 79 - 82:  10.861
  distance: 80 - 81:   6.264
  distance: 80 - 85:  27.792
  distance: 82 - 83:  32.495
  distance: 82 - 84:  12.394
  distance: 117 - 125:   3.188
  distance: 120 - 131:   3.324