Starting phenix.real_space_refine
on Sat Aug 23 10:30:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5k11_8193/08_2025/5k11_8193.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5k11_8193/08_2025/5k11_8193.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5k11_8193/08_2025/5k11_8193.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5k11_8193/08_2025/5k11_8193.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5k11_8193/08_2025/5k11_8193.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5k11_8193/08_2025/5k11_8193.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6334 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      38      5.16       5
     C    4016      2.51       5
     N    1074      2.21       5
     O    1204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6338
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3121
          Classifications: {'peptide': 397}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 12, 'TRANS': 384}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NDP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.78, per 1000 atoms: 0.28
  Number of scatterers: 6338
  At special positions: 0
  Unit cell: (103.455, 73.755, 82.17, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       6     15.00
     O    1204      8.00
     N    1074      7.00
     C    4016      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: 0.50
  Conformation dependent library (CDL) restraints added in 325.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 9 sheets defined
      49.1% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 29
      removed outlier: 3.526A  pdb=" N   GLU A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 54 through 68
      removed outlier: 3.656A  pdb=" N   LYS A  58 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA A  63 " --> pdb=" O   ASP A  59 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS A  66 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 86
      removed outlier: 3.591A  pdb=" N   PHE A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 186 through 204
    Processing helix  chain 'A' and resid 216 through 232
      removed outlier: 3.835A  pdb=" N   ASP A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASP A 225 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 241
      removed outlier: 4.474A  pdb=" N   GLN A 238 " --> pdb=" O   GLN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.610A  pdb=" N   MET A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 329 through 348
      removed outlier: 3.803A  pdb=" N   TRP A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A 345 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 369
      removed outlier: 3.786A  pdb=" N   PHE A 355 " --> pdb=" O   GLU A 351 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 387 through 391
      removed outlier: 3.711A  pdb=" N   TYR A 391 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 413
      removed outlier: 3.879A  pdb=" N   MET A 398 " --> pdb=" O   THR A 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 29
      removed outlier: 3.526A  pdb=" N   GLU B  24 " --> pdb=" O   ARG B  20 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 54 through 68
      removed outlier: 3.656A  pdb=" N   LYS B  58 " --> pdb=" O   ASP B  54 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS B  65 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS B  66 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 86
      removed outlier: 3.590A  pdb=" N   PHE B  86 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 186 through 204
    Processing helix  chain 'B' and resid 216 through 232
      removed outlier: 3.834A  pdb=" N   ASP B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASP B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 241
      removed outlier: 4.473A  pdb=" N   GLN B 238 " --> pdb=" O   GLN B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.610A  pdb=" N   MET B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 318
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 3.803A  pdb=" N   TRP B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 369
      removed outlier: 3.786A  pdb=" N   PHE B 355 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE B 367 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 381
    Processing helix  chain 'B' and resid 387 through 391
      removed outlier: 3.711A  pdb=" N   TYR B 391 " --> pdb=" O   ARG B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 413
      removed outlier: 3.878A  pdb=" N   MET B 398 " --> pdb=" O   THR B 394 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 14
      removed outlier: 4.933A  pdb=" N   ILE A   5 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ASP A  38 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLY A   7 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 9.169A  pdb=" N   HIS A  40 " --> pdb=" O   GLY A   7 " (cutoff:3.500A)
      removed outlier: 9.715A  pdb=" N   SER A   9 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 11.591A  pdb=" N   TYR A  42 " --> pdb=" O   SER A   9 " (cutoff:3.500A)
      removed outlier: 9.807A  pdb=" N   VAL A  11 " --> pdb=" O   TYR A  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 72
      removed outlier: 4.028A  pdb=" N   ALA A 307 " --> pdb=" O   LYS A  72 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ILE A 129 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 144
      removed outlier: 3.554A  pdb=" N   THR A 142 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR B 142 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 166
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208
      removed outlier: 6.351A  pdb=" N   LEU A 207 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 14
      removed outlier: 4.933A  pdb=" N   ILE B   5 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ASP B  38 " --> pdb=" O   ILE B   5 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLY B   7 " --> pdb=" O   ASP B  38 " (cutoff:3.500A)
      removed outlier: 9.169A  pdb=" N   HIS B  40 " --> pdb=" O   GLY B   7 " (cutoff:3.500A)
      removed outlier: 9.715A  pdb=" N   SER B   9 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
      removed outlier: 11.591A  pdb=" N   TYR B  42 " --> pdb=" O   SER B   9 " (cutoff:3.500A)
      removed outlier: 9.806A  pdb=" N   VAL B  11 " --> pdb=" O   TYR B  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72
      removed outlier: 4.027A  pdb=" N   ALA B 307 " --> pdb=" O   LYS B  72 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ILE B 129 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 208
      removed outlier: 6.351A  pdb=" N   LEU B 207 " --> pdb=" O   GLU B 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    310 hydrogen bonds defined for protein.
    900 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: 0.87

  Time building geometry restraints manager: 0.64 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: 1988
        1.34 -     1.46: 1296
        1.46 -     1.58: 3112
        1.58 -     1.70: 10
        1.70 -     1.82: 64
  Bond restraints: 6470
  Sorted by residual:
  bond pdb=" O2B NDP A 501 "
       pdb=" P2B NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.833  1.610  0.223 3.80e-02 6.93e+02 3.45e+01
  bond pdb=" O2B NDP B 501 "
       pdb=" P2B NDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.833  1.611  0.222 3.80e-02 6.93e+02 3.43e+01
  bond pdb=" O5D NDP A 501 "
       pdb=" PN  NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.757  1.609  0.148 3.50e-02 8.16e+02 1.79e+01
  bond pdb=" O5D NDP B 501 "
       pdb=" PN  NDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.757  1.610  0.147 3.50e-02 8.16e+02 1.77e+01
  bond pdb=" C2B NDP A 501 "
       pdb=" O2B NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.330  1.426 -0.096 2.90e-02 1.19e+03 1.10e+01
  ... (remaining 6465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.32: 8533
        3.32 -     6.64: 173
        6.64 -     9.96: 24
        9.96 -    13.27: 2
       13.27 -    16.59: 4
  Bond angle restraints: 8736
  Sorted by residual:
  angle pdb=" C5B NDP B 501 "
        pdb=" O5B NDP B 501 "
        pdb=" PA  NDP B 501 "
      ideal   model   delta    sigma   weight residual
     103.84  120.43  -16.59 1.91e+00 2.73e-01 7.51e+01
  angle pdb=" C5B NDP A 501 "
        pdb=" O5B NDP A 501 "
        pdb=" PA  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     103.84  120.40  -16.56 1.91e+00 2.73e-01 7.48e+01
  angle pdb=" PA  NDP B 501 "
        pdb=" O3  NDP B 501 "
        pdb=" PN  NDP B 501 "
      ideal   model   delta    sigma   weight residual
     107.74  120.34  -12.60 1.95e+00 2.62e-01 4.16e+01
  angle pdb=" PA  NDP A 501 "
        pdb=" O3  NDP A 501 "
        pdb=" PN  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     107.74  120.31  -12.57 1.95e+00 2.62e-01 4.14e+01
  angle pdb=" C5D NDP B 501 "
        pdb=" O5D NDP B 501 "
        pdb=" PN  NDP B 501 "
      ideal   model   delta    sigma   weight residual
     104.93  120.48  -15.55 2.66e+00 1.41e-01 3.42e+01
  ... (remaining 8731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.22: 3786
       29.22 -    58.44: 42
       58.44 -    87.66: 12
       87.66 -   116.88: 0
      116.88 -   146.11: 2
  Dihedral angle restraints: 3842
    sinusoidal: 1564
      harmonic: 2278
  Sorted by residual:
  dihedral pdb=" CA  PHE B 334 "
           pdb=" C   PHE B 334 "
           pdb=" N   ALA B 335 "
           pdb=" CA  ALA B 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.10   24.90     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  PHE A 334 "
           pdb=" C   PHE A 334 "
           pdb=" N   ALA A 335 "
           pdb=" CA  ALA A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.14   24.86     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  ALA B 241 "
           pdb=" C   ALA B 241 "
           pdb=" N   GLN B 242 "
           pdb=" CA  GLN B 242 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.49  -24.51     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 3839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 595
       0.050 -    0.100: 279
       0.100 -    0.151: 66
       0.151 -    0.201: 10
       0.201 -    0.251: 4
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CB  ILE A 244 "
            pdb=" CA  ILE A 244 "
            pdb=" CG1 ILE A 244 "
            pdb=" CG2 ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  ILE B 244 "
            pdb=" CA  ILE B 244 "
            pdb=" CG1 ILE B 244 "
            pdb=" CG2 ILE B 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  VAL A 255 "
            pdb=" CA  VAL A 255 "
            pdb=" CG1 VAL A 255 "
            pdb=" CG2 VAL A 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 951 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 192 "   -0.022 2.00e-02 2.50e+03   2.06e-02 7.41e+00
        pdb=" CG  PHE A 192 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 192 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 192 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 192 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 192 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 192 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 192 "    0.022 2.00e-02 2.50e+03   2.03e-02 7.23e+00
        pdb=" CG  PHE B 192 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 192 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 192 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 192 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 192 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 192 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  32 "    0.013 2.00e-02 2.50e+03   1.67e-02 4.90e+00
        pdb=" CG  PHE A  32 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  32 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  32 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  32 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  32 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  32 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 148
        2.63 -     3.20: 6423
        3.20 -     3.76: 10358
        3.76 -     4.33: 15209
        4.33 -     4.90: 23412
  Nonbonded interactions: 55550
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  29 "
            pdb=" OD1 ASP A 399 "
     model   vdw
     2.061 3.120
  nonbonded pdb=" NZ  LYS B  29 "
            pdb=" OD1 ASP B 399 "
     model   vdw
     2.061 3.120
  nonbonded pdb=" ND2 ASN B 184 "
            pdb=" OH  TYR B 219 "
     model   vdw
     2.137 3.120
  nonbonded pdb=" ND2 ASN A 184 "
            pdb=" OH  TYR A 219 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" ND2 ASN B 116 "
            pdb=" O   ILE B 367 "
     model   vdw
     2.148 3.120
  ... (remaining 55545 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.420
  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:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
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      :  0.012   0.223   6470  Z= 0.493
  Angle     :  1.235  16.593   8736  Z= 0.649
  Chirality :  0.059   0.251    954
  Planarity :  0.006   0.050   1104
  Dihedral  : 12.123 146.105   2378
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 29.45
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  6.14 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.21 %
    Favored  : 98.49 %
  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: -4.89 (0.22), residues: 782
  helix: -3.96 (0.17), residues: 326
  sheet: -2.87 (0.31), residues: 144
  loop : -2.27 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG B  49 
 TYR   0.035   0.004   TYR B 231 
 PHE   0.047   0.005   PHE A 192 
 TRP   0.025   0.005   TRP A  92 
 HIS   0.012   0.004   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.01186 ( 6470)
  covalent geometry    : angle       1.23492 ( 8736)
  hydrogen bonds       : bond        0.32255 (  302)
  hydrogen bonds       : angle      12.62400 (  900)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 205
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 VAL cc_start: 0.8490 (m) cc_final: 0.8000 (p)
REVERT: A  257 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8344 (tp-100)
REVERT: B  255 VAL cc_start: 0.8493 (m) cc_final: 0.8022 (p)
REVERT: B  257 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8323 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1087
  time to fit residues: 26.8978
Evaluate side-chains
  107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:   40.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0010
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   overall best weight:    4.1792

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
A  96 ASN
** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
A 228 GLN
A 271 ASN
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 315 HIS
A 385 ASN
B  40 HIS
B  96 ASN
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 ASN
B 228 GLN
B 271 ASN
** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 315 HIS
B 385 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.063579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.050612 restraints weight = 29609.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.052487 restraints weight = 19924.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.053921 restraints weight = 14602.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.054953 restraints weight = 11380.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.055826 restraints weight = 9319.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.4497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   6470  Z= 0.209
  Angle     :  0.838   6.499   8736  Z= 0.440
  Chirality :  0.050   0.196    954
  Planarity :  0.005   0.051   1104
  Dihedral  : 10.828 151.532    860
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 21.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.24 %
    Favored  : 86.71 %
  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: -2.59 (0.26), residues: 782
  helix: -1.50 (0.23), residues: 364
  sheet: -2.29 (0.30), residues: 192
  loop : -0.94 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 314 
 TYR   0.020   0.002   TYR A 219 
 PHE   0.024   0.003   PHE B 227 
 TRP   0.034   0.004   TRP B  23 
 HIS   0.008   0.002   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6470)
  covalent geometry    : angle       0.83751 ( 8736)
  hydrogen bonds       : bond        0.05943 (  302)
  hydrogen bonds       : angle       6.76983 (  900)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.9129 (tpt) cc_final: 0.8919 (tpt)
REVERT: A  254 MET cc_start: 0.8375 (tpp) cc_final: 0.7890 (tpp)
REVERT: A  255 VAL cc_start: 0.9675 (m) cc_final: 0.9185 (p)
REVERT: A  257 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8466 (tm-30)
REVERT: A  365 GLU cc_start: 0.8920 (pp20) cc_final: 0.8624 (pp20)
REVERT: B   35 VAL cc_start: 0.9415 (p) cc_final: 0.9191 (m)
REVERT: B  254 MET cc_start: 0.8381 (tpp) cc_final: 0.7911 (tpp)
REVERT: B  255 VAL cc_start: 0.9674 (m) cc_final: 0.9176 (p)
REVERT: B  257 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8488 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 135
  average time/residue: 0.0836
  time to fit residues: 14.4024
Evaluate side-chains
  107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  107 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 101 ASN
A 309 HIS
B  68 ASN
B 101 ASN
B 309 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.061555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.049263 restraints weight = 30390.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.051065 restraints weight = 19865.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.052465 restraints weight = 14318.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.053474 restraints weight = 10999.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.054265 restraints weight = 8902.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6470  Z= 0.186
  Angle     :  0.775   7.735   8736  Z= 0.403
  Chirality :  0.047   0.161    954
  Planarity :  0.004   0.038   1104
  Dihedral  : 10.145 150.800    860
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.14 %
    Favored  : 84.29 %
  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: -1.34 (0.29), residues: 782
  helix: -0.33 (0.27), residues: 366
  sheet: -1.85 (0.33), residues: 188
  loop : -0.46 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  82 
 TYR   0.016   0.002   TYR A 219 
 PHE   0.020   0.002   PHE A 355 
 TRP   0.031   0.003   TRP B  23 
 HIS   0.005   0.002   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 6470)
  covalent geometry    : angle       0.77476 ( 8736)
  hydrogen bonds       : bond        0.04274 (  302)
  hydrogen bonds       : angle       6.00904 (  900)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8171 (mp)
REVERT: A  254 MET cc_start: 0.8136 (tpp) cc_final: 0.7403 (tpp)
REVERT: A  293 SER cc_start: 0.9252 (t) cc_final: 0.8235 (m)
REVERT: A  365 GLU cc_start: 0.8857 (pp20) cc_final: 0.8222 (pp20)
REVERT: A  396 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9006 (mt-10)
REVERT: B   23 TRP cc_start: 0.9085 (t-100) cc_final: 0.8452 (t-100)
REVERT: B   65 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9132 (mtpp)
REVERT: B  112 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8226 (mp)
REVERT: B  254 MET cc_start: 0.8143 (tpp) cc_final: 0.7429 (tpp)
REVERT: B  396 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9000 (mt-10)
  outliers start: 17
  outliers final: 6
  residues processed: 134
  average time/residue: 0.0899
  time to fit residues: 15.0840
Evaluate side-chains
  108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  252 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:   30.0000
   chunk 48 optimal weight:   40.0000
   chunk 67 optimal weight:   10.0000
   chunk 59 optimal weight:   20.0000
   chunk 73 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 36 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:   30.0000
   chunk 60 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    7.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.060256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.048330 restraints weight = 31954.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.050135 restraints weight = 20371.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.051528 restraints weight = 14580.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.052529 restraints weight = 11177.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.053330 restraints weight = 9053.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.6096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6470  Z= 0.215
  Angle     :  0.788   6.573   8736  Z= 0.412
  Chirality :  0.050   0.356    954
  Planarity :  0.004   0.046   1104
  Dihedral  :  9.961 150.220    860
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 21.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.52 %
    Favored  : 80.36 %
  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: -0.89 (0.30), residues: 782
  helix: -0.01 (0.27), residues: 364
  sheet: -1.66 (0.37), residues: 170
  loop : -0.28 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 314 
 TYR   0.012   0.002   TYR B  34 
 PHE   0.032   0.002   PHE B 355 
 TRP   0.016   0.002   TRP A  23 
 HIS   0.005   0.002   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 6470)
  covalent geometry    : angle       0.78784 ( 8736)
  hydrogen bonds       : bond        0.04358 (  302)
  hydrogen bonds       : angle       5.59579 (  900)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 TRP cc_start: 0.9101 (t-100) cc_final: 0.8597 (t-100)
REVERT: A   65 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9288 (mttt)
REVERT: A  110 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7145 (tm-30)
REVERT: A  254 MET cc_start: 0.7709 (tpp) cc_final: 0.7018 (tpp)
REVERT: A  396 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9043 (mt-10)
REVERT: B   22 ILE cc_start: 0.9733 (OUTLIER) cc_final: 0.9477 (tp)
REVERT: B   65 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9262 (mttt)
REVERT: B  199 MET cc_start: 0.9216 (tpt) cc_final: 0.8935 (tmm)
REVERT: B  254 MET cc_start: 0.7687 (tpp) cc_final: 0.6984 (tpp)
REVERT: B  396 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9073 (mt-10)
  outliers start: 14
  outliers final: 5
  residues processed: 114
  average time/residue: 0.0962
  time to fit residues: 14.0802
Evaluate side-chains
  97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LYS
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  252 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 72 optimal weight:    6.9990
   chunk 17 optimal weight:   40.0000
   chunk 7 optimal weight:   50.0000
   chunk 56 optimal weight:   40.0000
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 257 GLN
B 257 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.059959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.048411 restraints weight = 32011.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.050279 restraints weight = 20508.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.051654 restraints weight = 14625.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.052622 restraints weight = 11185.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.053400 restraints weight = 9070.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.6625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6470  Z= 0.200
  Angle     :  0.758   9.285   8736  Z= 0.389
  Chirality :  0.048   0.275    954
  Planarity :  0.004   0.046   1104
  Dihedral  :  9.864 156.715    860
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.82 %
    Favored  : 80.36 %
  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: -0.43 (0.30), residues: 782
  helix:  0.36 (0.27), residues: 374
  sheet: -0.95 (0.41), residues: 150
  loop : -0.58 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 314 
 TYR   0.013   0.002   TYR A  34 
 PHE   0.014   0.002   PHE B 144 
 TRP   0.017   0.002   TRP A  23 
 HIS   0.005   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6470)
  covalent geometry    : angle       0.75839 ( 8736)
  hydrogen bonds       : bond        0.04272 (  302)
  hydrogen bonds       : angle       5.27349 (  900)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LYS cc_start: 0.9602 (OUTLIER) cc_final: 0.9290 (mttt)
REVERT: A   96 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.9195 (m110)
REVERT: A  342 HIS cc_start: 0.9007 (t70) cc_final: 0.8548 (t-170)
REVERT: A  396 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9066 (mt-10)
REVERT: B   18 MET cc_start: 0.8886 (mtm) cc_final: 0.8675 (mtp)
REVERT: B   65 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.9303 (mttt)
REVERT: B  130 ILE cc_start: 0.9308 (mp) cc_final: 0.8932 (tt)
REVERT: B  342 HIS cc_start: 0.9033 (t70) cc_final: 0.8577 (t-170)
REVERT: B  396 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9091 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0977
  time to fit residues: 13.8916
Evaluate side-chains
  101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LYS
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  252 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
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: 65.0102 > 50:
  distance: 34 - 39:  22.125
  distance: 39 - 40:  12.059
  distance: 40 - 41:  33.975
  distance: 40 - 43:  40.063
  distance: 41 - 42:  32.513
  distance: 41 - 47:  41.261
  distance: 43 - 44:  15.223
  distance: 44 - 45:  32.809
  distance: 44 - 46:  22.257
  distance: 47 - 48:  31.726
  distance: 48 - 49:  12.103
  distance: 48 - 51:  24.861
  distance: 49 - 59:   4.482
  distance: 51 - 52:   7.438
  distance: 52 - 53:  48.478
  distance: 52 - 54:  32.740
  distance: 53 - 55:  15.169
  distance: 54 - 56:  14.763
  distance: 55 - 57:  10.818
  distance: 56 - 57:  15.804
  distance: 57 - 58:  18.604
  distance: 59 - 60:  13.262
  distance: 60 - 61:  13.094
  distance: 60 - 63:  26.141
  distance: 61 - 62:  20.722
  distance: 61 - 67:  24.518
  distance: 63 - 64:  57.476
  distance: 64 - 66:  13.269
  distance: 67 - 68:  16.995
  distance: 68 - 69:  28.538
  distance: 68 - 71:  25.156
  distance: 69 - 70:  30.860
  distance: 69 - 73:  21.428
  distance: 73 - 74:  27.500
  distance: 74 - 75:  13.883
  distance: 74 - 77:  21.866
  distance: 75 - 76:  12.941
  distance: 75 - 80:  12.427
  distance: 77 - 78:  37.125
  distance: 77 - 79:  13.884
  distance: 80 - 81:  36.428
  distance: 81 - 82:  33.988
  distance: 81 - 84:  12.990
  distance: 82 - 83:   9.802
  distance: 82 - 89:  37.902
  distance: 84 - 85:  34.035
  distance: 85 - 86:  35.804
  distance: 86 - 87:  13.238
  distance: 87 - 88:  11.225
  distance: 89 - 90:  28.020
  distance: 90 - 91:  24.106
  distance: 90 - 93:  38.552
  distance: 91 - 92:  40.670
  distance: 91 - 97:  25.849
  distance: 94 - 95:  33.383
  distance: 94 - 96:  10.547
  distance: 97 - 98:  32.218
  distance: 98 - 99:  12.560
  distance: 98 - 101:  28.812
  distance: 99 - 100:  28.912
  distance: 99 - 104:  47.705
  distance: 101 - 102:  32.656
  distance: 101 - 103:  50.195
  distance: 104 - 105:  22.120
  distance: 105 - 106:  31.216
  distance: 105 - 108:  32.819
  distance: 106 - 107:  28.060
  distance: 106 - 112:   5.172
  distance: 108 - 109:  10.731
  distance: 108 - 110:  36.225
  distance: 109 - 111:  32.516
  distance: 112 - 113:  54.852
  distance: 113 - 114:  51.357
  distance: 113 - 116:  41.100
  distance: 114 - 115:  17.369
  distance: 114 - 120:  24.991
  distance: 116 - 117:  11.887
  distance: 117 - 118:  29.284
  distance: 117 - 119:  11.079