Starting phenix.real_space_refine
on Mon Nov 17 13:28:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp2_32667/11_2025/7wp2_32667.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp2_32667/11_2025/7wp2_32667.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp2_32667/11_2025/7wp2_32667.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp2_32667/11_2025/7wp2_32667.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp2_32667/11_2025/7wp2_32667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp2_32667/11_2025/7wp2_32667.map"
  }
  resolution = 3.52
  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=   0.011
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      14      5.16       5
     C    2090      2.51       5
     N     554      2.21       5
     O     641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3299
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 796
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1017
          Classifications: {'peptide': 131}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "F"
      Number of atoms: 1458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1458
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
    Chain: "A"
      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: 1.28, per 1000 atoms: 0.39
  Number of scatterers: 3299
  At special positions: 0
  Unit cell: (76.244, 79.356, 80.912, 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      14     16.00
     O     641      8.00
     N     554      7.00
     C    2090      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 343 "
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 151.5 milliseconds
  

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  754

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 9 sheets defined
      2.6% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.905A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'F' and resid 405 through 410
      removed outlier: 4.037A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.623A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18
    Processing sheet with id=AA3, first strand: chain 'L' and resid 22 through 23
      removed outlier: 3.520A  pdb=" N   SER L  69 " --> pdb=" O   SER L  72 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER L  74 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 50
      removed outlier: 6.564A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR L  89 " --> pdb=" O   TYR L  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.785A  pdb=" N   TYR H  59 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 358
      removed outlier: 3.880A  pdb=" N   ASN F 354 " --> pdb=" O   SER F 399 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   SER F 399 " --> pdb=" O   ASN F 354 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LYS F 356 " --> pdb=" O   ALA F 397 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   CYS F 432 " --> pdb=" O   LEU F 513 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454

    69 hydrogen bonds defined for protein.
    159 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: 0.35

  Time building geometry restraints manager: 0.38 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: 1049
        1.34 -     1.46: 843
        1.46 -     1.57: 1473
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3383
  Sorted by residual:
  bond pdb=" C1  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.87e+00
  bond pdb=" C   LYS F 462 "
       pdb=" N   PRO F 463 "
    ideal  model  delta    sigma   weight residual
    1.332  1.351 -0.019 1.12e-02 7.97e+03 3.02e+00
  bond pdb=" CB  CYS L  90 "
       pdb=" SG  CYS L  90 "
    ideal  model  delta    sigma   weight residual
    1.808  1.752  0.056 3.30e-02 9.18e+02 2.85e+00
  bond pdb=" C   ASN L  55 "
       pdb=" N   ARG L  56 "
    ideal  model  delta    sigma   weight residual
    1.332  1.271  0.060 3.60e-02 7.72e+02 2.81e+00
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.09e+00
  ... (remaining 3378 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 4496
        2.54 -     5.07: 85
        5.07 -     7.61: 9
        7.61 -    10.15: 3
       10.15 -    12.69: 1
  Bond angle restraints: 4594
  Sorted by residual:
  angle pdb=" C   GLY L  52 "
        pdb=" N   ASN L  53 "
        pdb=" CA  ASN L  53 "
      ideal   model   delta    sigma   weight residual
     121.54  130.20   -8.66 1.91e+00 2.74e-01 2.06e+01
  angle pdb=" CA  LEU F 387 "
        pdb=" CB  LEU F 387 "
        pdb=" CG  LEU F 387 "
      ideal   model   delta    sigma   weight residual
     116.30  128.99  -12.69 3.50e+00 8.16e-02 1.31e+01
  angle pdb=" C   TYR F 369 "
        pdb=" N   ASN F 370 "
        pdb=" CA  ASN F 370 "
      ideal   model   delta    sigma   weight residual
     122.07  127.10   -5.03 1.43e+00 4.89e-01 1.24e+01
  angle pdb=" C   ASP F 364 "
        pdb=" N   TYR F 365 "
        pdb=" CA  TYR F 365 "
      ideal   model   delta    sigma   weight residual
     121.54  127.45   -5.91 1.91e+00 2.74e-01 9.58e+00
  angle pdb=" C   SER H  52 "
        pdb=" N   PHE H  53 "
        pdb=" CA  PHE H  53 "
      ideal   model   delta    sigma   weight residual
     120.44  124.43   -3.99 1.30e+00 5.92e-01 9.40e+00
  ... (remaining 4589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 1779
       17.78 -    35.55: 173
       35.55 -    53.33: 25
       53.33 -    71.11: 5
       71.11 -    88.88: 3
  Dihedral angle restraints: 1985
    sinusoidal: 780
      harmonic: 1205
  Sorted by residual:
  dihedral pdb=" CA  ASP H 113 "
           pdb=" C   ASP H 113 "
           pdb=" N   TYR H 114 "
           pdb=" CA  TYR H 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.46  -29.54     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  PHE F 338 "
           pdb=" C   PHE F 338 "
           pdb=" N   GLY F 339 "
           pdb=" CA  GLY F 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.35   24.65     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  ILE F 472 "
           pdb=" C   ILE F 472 "
           pdb=" N   TYR F 473 "
           pdb=" CA  TYR F 473 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.39  -23.61     0      5.00e+00 4.00e-02 2.23e+01
  ... (remaining 1982 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 306
       0.047 -    0.094: 137
       0.094 -    0.141: 34
       0.141 -    0.188: 7
       0.188 -    0.235: 5
  Chirality restraints: 489
  Sorted by residual:
  chirality pdb=" CB  ILE H  70 "
            pdb=" CA  ILE H  70 "
            pdb=" CG1 ILE H  70 "
            pdb=" CG2 ILE H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  THR H  91 "
            pdb=" CA  THR H  91 "
            pdb=" OG1 THR H  91 "
            pdb=" CG2 THR H  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  VAL H 100 "
            pdb=" CA  VAL H 100 "
            pdb=" CG1 VAL H 100 "
            pdb=" CG2 VAL H 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 486 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN F 498 "   -0.046 5.00e-02 4.00e+02   6.98e-02 7.79e+00
        pdb=" N   PRO F 499 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO F 499 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO F 499 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  13 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.74e+00
        pdb=" N   PRO L  14 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO L  14 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO L  14 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 462 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO F 463 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO F 463 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO F 463 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 909
        2.79 -     3.32: 2630
        3.32 -     3.85: 5262
        3.85 -     4.37: 5959
        4.37 -     4.90: 10778
  Nonbonded interactions: 25538
  Sorted by model distance:
  nonbonded pdb=" OH  TYR L  93 "
            pdb=" OD1 ASP H 113 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG1 THR F 415 "
            pdb=" OD1 ASP F 420 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR L  38 "
            pdb=" OE1 GLN L  91 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR L  51 "
            pdb=" O   THR F 415 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" NE2 HIS L  36 "
            pdb=" O   ASN H 115 "
     model   vdw
     2.288 3.120
  ... (remaining 25533 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             19.270
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.770
  Find NCS groups from input model:        0.020
  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:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
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      :  0.007   0.060   3387  Z= 0.304
  Angle     :  0.911  12.687   4604  Z= 0.500
  Chirality :  0.056   0.235    489
  Planarity :  0.007   0.070    594
  Dihedral  : 13.822  88.882   1225
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  9.66 %
    Favored  : 90.06 %
  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 are not related in a simple way.
  whole: -4.60 (0.34), residues: 416
  helix: -5.07 (0.26), residues: 20
  sheet: -2.60 (0.38), residues: 162
  loop : -3.28 (0.31), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 408 
 TYR   0.028   0.003   TYR H 103 
 PHE   0.018   0.002   PHE F 490 
 TRP   0.021   0.002   TRP F 353 
 HIS   0.004   0.002   HIS F 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 ( 3383)
  covalent geometry    : angle       0.90724 ( 4594)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       1.70877 (    4)
  hydrogen bonds       : bond        0.26493 (   69)
  hydrogen bonds       : angle      10.34313 (  159)
  link_BETA1-4         : bond        0.00720 (    1)
  link_BETA1-4         : angle       1.70846 (    3)
  link_NAG-ASN         : bond        0.00247 (    1)
  link_NAG-ASN         : angle       2.65504 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.128 
Fit side-chains
REVERT: L   93 TYR cc_start: 0.8650 (t80) cc_final: 0.8437 (t80)
REVERT: H   19 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6860 (ttp80)
REVERT: H   29 PHE cc_start: 0.9274 (t80) cc_final: 0.9067 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.0878
  time to fit residues: 7.9747
Evaluate side-chains
  61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
L  55 ASN
F 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.131572 restraints weight = 4674.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134830 restraints weight = 2495.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.136999 restraints weight = 1638.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138270 restraints weight = 1215.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.139390 restraints weight = 992.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3387  Z= 0.154
  Angle     :  0.601   7.885   4604  Z= 0.313
  Chirality :  0.043   0.139    489
  Planarity :  0.005   0.047    594
  Dihedral  :  6.820  54.457    516
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.77 %
    Favored  : 83.24 %
  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 are not related in a simple way.
  whole: -3.96 (0.35), residues: 416
  helix: -4.82 (0.44), residues: 20
  sheet: -1.92 (0.40), residues: 151
  loop : -3.01 (0.33), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  56 
 TYR   0.012   0.001   TYR H 103 
 PHE   0.013   0.001   PHE F 338 
 TRP   0.011   0.001   TRP F 353 
 HIS   0.003   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3383)
  covalent geometry    : angle       0.59887 ( 4594)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       1.26197 (    4)
  hydrogen bonds       : bond        0.04417 (   69)
  hydrogen bonds       : angle       7.33011 (  159)
  link_BETA1-4         : bond        0.00444 (    1)
  link_BETA1-4         : angle       1.08267 (    3)
  link_NAG-ASN         : bond        0.00383 (    1)
  link_NAG-ASN         : angle       1.46339 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.135 
Fit side-chains
REVERT: L   93 TYR cc_start: 0.8654 (t80) cc_final: 0.8380 (t80)
REVERT: H   19 ARG cc_start: 0.7579 (ttm170) cc_final: 0.6979 (ttp80)
REVERT: F  417 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7660 (ttmm)
  outliers start: 7
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0910
  time to fit residues: 6.9123
Evaluate side-chains
  58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain F residue  415 THR
Chi-restraints excluded: chain F residue  417 LYS
Chi-restraints excluded: chain F residue  483 VAL
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0270
   chunk 34 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 15 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
H  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.155616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.139012 restraints weight = 4579.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.142385 restraints weight = 2401.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144594 restraints weight = 1553.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145895 restraints weight = 1144.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147032 restraints weight = 927.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3387  Z= 0.129
  Angle     :  0.562   7.674   4604  Z= 0.289
  Chirality :  0.042   0.139    489
  Planarity :  0.004   0.035    594
  Dihedral  :  6.270  49.311    516
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 15.06 %
    Favored  : 80.97 %
  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 are not related in a simple way.
  whole: -3.67 (0.36), residues: 416
  helix: -4.72 (0.50), residues: 20
  sheet: -1.75 (0.41), residues: 148
  loop : -2.78 (0.33), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 454 
 TYR   0.011   0.001   TYR F 369 
 PHE   0.010   0.001   PHE F 338 
 TRP   0.009   0.001   TRP F 353 
 HIS   0.002   0.001   HIS F 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3383)
  covalent geometry    : angle       0.55993 ( 4594)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       1.10996 (    4)
  hydrogen bonds       : bond        0.03417 (   69)
  hydrogen bonds       : angle       6.53337 (  159)
  link_BETA1-4         : bond        0.00340 (    1)
  link_BETA1-4         : angle       0.96937 (    3)
  link_NAG-ASN         : bond        0.00382 (    1)
  link_NAG-ASN         : angle       1.23336 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.144 
Fit side-chains
REVERT: L   93 TYR cc_start: 0.8641 (t80) cc_final: 0.8402 (t80)
REVERT: H   19 ARG cc_start: 0.7602 (ttm170) cc_final: 0.7291 (ttp-170)
REVERT: H   94 TYR cc_start: 0.8077 (m-80) cc_final: 0.7478 (m-80)
REVERT: F  417 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7622 (ttmm)
  outliers start: 14
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0794
  time to fit residues: 6.3529
Evaluate side-chains
  62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   69 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  415 THR
Chi-restraints excluded: chain F residue  417 LYS
Chi-restraints excluded: chain F residue  483 VAL
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0470
   overall best weight:    0.5676

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

Flipped N/Q/H residues before XYZ refinement:
F 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.153952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.136620 restraints weight = 4582.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.140040 restraints weight = 2467.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.142292 restraints weight = 1622.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.143755 restraints weight = 1205.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144829 restraints weight = 974.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3387  Z= 0.173
  Angle     :  0.584   7.680   4604  Z= 0.300
  Chirality :  0.043   0.142    489
  Planarity :  0.004   0.033    594
  Dihedral  :  6.035  44.609    516
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 13.64 %
    Favored  : 80.40 %
  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 are not related in a simple way.
  whole: -3.50 (0.37), residues: 416
  helix: -4.67 (0.52), residues: 20
  sheet: -1.63 (0.41), residues: 150
  loop : -2.66 (0.34), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 454 
 TYR   0.010   0.001   TYR F 369 
 PHE   0.014   0.001   PHE F 338 
 TRP   0.010   0.001   TRP F 353 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3383)
  covalent geometry    : angle       0.58207 ( 4594)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       1.10630 (    4)
  hydrogen bonds       : bond        0.03289 (   69)
  hydrogen bonds       : angle       6.22017 (  159)
  link_BETA1-4         : bond        0.00263 (    1)
  link_BETA1-4         : angle       0.89585 (    3)
  link_NAG-ASN         : bond        0.00428 (    1)
  link_NAG-ASN         : angle       1.45800 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.179 
Fit side-chains
REVERT: L   93 TYR cc_start: 0.8699 (t80) cc_final: 0.8412 (t80)
REVERT: H   13 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5765 (tt0)
REVERT: H   19 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7285 (ttp-170)
REVERT: H   94 TYR cc_start: 0.8217 (m-80) cc_final: 0.7471 (m-80)
REVERT: F  338 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6651 (p90)
REVERT: F  417 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7679 (ttmm)
  outliers start: 21
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0691
  time to fit residues: 5.8656
Evaluate side-chains
  67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   69 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   13 GLN
Chi-restraints excluded: chain H residue  112 LEU
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain F residue  338 PHE
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  415 THR
Chi-restraints excluded: chain F residue  417 LYS
Chi-restraints excluded: chain F residue  483 VAL
Chi-restraints excluded: chain F residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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: 68.639 > 50:
  distance: 7 - 9:  30.664
  distance: 9 - 10:  30.094
  distance: 10 - 11:  21.731
  distance: 11 - 12:  20.925
  distance: 11 - 13:   4.015
  distance: 12 - 151:  31.488
  distance: 13 - 14:  46.093
  distance: 14 - 15:  38.538
  distance: 14 - 17:  19.176
  distance: 15 - 16:  26.205
  distance: 15 - 20:  30.243
  distance: 17 - 19:  18.573
  distance: 20 - 21:  21.412
  distance: 20 - 154:  22.213
  distance: 21 - 22:  31.479
  distance: 21 - 24:  35.575
  distance: 22 - 27:  57.511
  distance: 24 - 25:  44.604
  distance: 24 - 26:  29.951
  distance: 27 - 28:  35.559
  distance: 28 - 29:  15.871
  distance: 28 - 31:  26.186
  distance: 29 - 30:  35.973
  distance: 29 - 36:  33.203
  distance: 31 - 32:  38.538
  distance: 32 - 33:  19.171
  distance: 33 - 34:  23.218
  distance: 33 - 35:  16.785
  distance: 36 - 37:  20.639
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