Starting phenix.real_space_refine
on Wed Mar  5 22:25:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx1_37897/03_2025/8wx1_37897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx1_37897/03_2025/8wx1_37897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx1_37897/03_2025/8wx1_37897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx1_37897/03_2025/8wx1_37897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx1_37897/03_2025/8wx1_37897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx1_37897/03_2025/8wx1_37897.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.038
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      23      5.16       5
     C    2593      2.51       5
     N     640      2.21       5
     O     670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3926
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3926
          Classifications: {'peptide': 500}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 25, 'TRANS': 474}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.70, per 1000 atoms: 0.69
  Number of scatterers: 3926
  At special positions: 0
  Unit cell: (79.68, 74.1467, 69.72, 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      23     16.00
     O     670      8.00
     N     640      7.00
     C    2593      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 523 " - pdb=" SG  CYS A 533 " 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
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 420.7 milliseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  926

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 1 sheets defined
      79.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 61
      removed outlier: 4.118A  pdb=" N   ASN A  55 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   VAL A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 97
      Proline residue:  A  88  - end of helix
      removed outlier: 4.076A  pdb=" N   TYR A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 123
    Processing helix  chain 'A' and resid 123 through 131
      removed outlier: 3.586A  pdb=" N   CYS A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 187
    Processing helix  chain 'A' and resid 191 through 224
    Processing helix  chain 'A' and resid 225 through 247
      removed outlier: 3.884A  pdb=" N   GLY A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
    Processing helix  chain 'A' and resid 300 through 341
      Proline residue:  A 316  - end of helix
      Proline residue:  A 323  - end of helix
      removed outlier: 3.641A  pdb=" N   HIS A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 399
      removed outlier: 3.677A  pdb=" N   LEU A 383 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 384 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      Proline residue:  A 385  - end of helix
      Proline residue:  A 393  - end of helix
    Processing helix  chain 'A' and resid 403 through 435
      removed outlier: 3.597A  pdb=" N   ALA A 435 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 457 through 483
      removed outlier: 4.556A  pdb=" N   GLN A 461 " --> pdb=" O   TRP A 457 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 488 through 515
    Processing helix  chain 'A' and resid 535 through 566
    Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 443
      removed outlier: 3.961A  pdb=" N   ILE A 443 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 446 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    939 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: 0.91

  Time building geometry restraints manager: 1.03 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: 1194
        1.34 -     1.46: 919
        1.46 -     1.58: 1879
        1.58 -     1.70: 0
        1.70 -     1.81: 37
  Bond restraints: 4029
  Sorted by residual:
  bond pdb=" C   SER A 154 "
       pdb=" N   PRO A 155 "
    ideal  model  delta    sigma   weight residual
    1.331  1.362 -0.031 1.27e-02 6.20e+03 5.85e+00
  bond pdb=" C   VAL A 322 "
       pdb=" N   PRO A 323 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.77e+00
  bond pdb=" C   ILE A 474 "
       pdb=" N   PRO A 475 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.023 1.28e-02 6.10e+03 3.19e+00
  bond pdb=" C   ALA A  87 "
       pdb=" N   PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.20e-02 6.94e+03 3.12e+00
  bond pdb=" C   LEU A 315 "
       pdb=" N   PRO A 316 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.28e-02 6.10e+03 2.87e+00
  ... (remaining 4024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 5103
        1.29 -     2.59: 298
        2.59 -     3.88: 59
        3.88 -     5.17: 20
        5.17 -     6.47: 7
  Bond angle restraints: 5487
  Sorted by residual:
  angle pdb=" N   VAL A 187 "
        pdb=" CA  VAL A 187 "
        pdb=" C   VAL A 187 "
      ideal   model   delta    sigma   weight residual
     111.91  108.05    3.86 8.90e-01 1.26e+00 1.88e+01
  angle pdb=" C   GLN A 458 "
        pdb=" N   ILE A 459 "
        pdb=" CA  ILE A 459 "
      ideal   model   delta    sigma   weight residual
     120.33  123.30   -2.97 8.00e-01 1.56e+00 1.38e+01
  angle pdb=" C   VAL A 322 "
        pdb=" CA  VAL A 322 "
        pdb=" CB  VAL A 322 "
      ideal   model   delta    sigma   weight residual
     113.70  110.40    3.30 9.50e-01 1.11e+00 1.21e+01
  angle pdb=" C   TRP A 152 "
        pdb=" N   SER A 153 "
        pdb=" CA  SER A 153 "
      ideal   model   delta    sigma   weight residual
     122.74  127.50   -4.76 1.44e+00 4.82e-01 1.09e+01
  angle pdb=" CA  ARG A 366 "
        pdb=" C   ARG A 366 "
        pdb=" N   ILE A 367 "
      ideal   model   delta    sigma   weight residual
     114.17  118.88   -4.71 1.45e+00 4.76e-01 1.05e+01
  ... (remaining 5482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2100
       17.16 -    34.33: 207
       34.33 -    51.49: 31
       51.49 -    68.66: 6
       68.66 -    85.82: 4
  Dihedral angle restraints: 2348
    sinusoidal: 906
      harmonic: 1442
  Sorted by residual:
  dihedral pdb=" CA  MET A 188 "
           pdb=" C   MET A 188 "
           pdb=" N   ASP A 189 "
           pdb=" CA  ASP A 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.74  -32.26     0      5.00e+00 4.00e-02 4.16e+01
  dihedral pdb=" CA  CYS A 273 "
           pdb=" C   CYS A 273 "
           pdb=" N   PRO A 274 "
           pdb=" CA  PRO A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.53   16.47     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  ASN A 346 "
           pdb=" CB  ASN A 346 "
           pdb=" CG  ASN A 346 "
           pdb=" OD1 ASN A 346 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -174.37  -65.63     2      2.00e+01 2.50e-03 9.96e+00
  ... (remaining 2345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 436
       0.027 -    0.054: 100
       0.054 -    0.081: 68
       0.081 -    0.109: 20
       0.109 -    0.136: 5
  Chirality restraints: 629
  Sorted by residual:
  chirality pdb=" CA  ILE A 224 "
            pdb=" N   ILE A 224 "
            pdb=" C   ILE A 224 "
            pdb=" CB  ILE A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 344 "
            pdb=" N   ILE A 344 "
            pdb=" C   ILE A 344 "
            pdb=" CB  ILE A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  PRO A 368 "
            pdb=" N   PRO A 368 "
            pdb=" C   PRO A 368 "
            pdb=" CB  PRO A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 626 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  26 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A  27 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 214 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.30e+00
        pdb=" C   LEU A 214 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 214 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 215 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 439 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO A 440 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 440 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 440 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1147
        2.82 -     3.34: 4189
        3.34 -     3.86: 6800
        3.86 -     4.38: 7128
        4.38 -     4.90: 12352
  Nonbonded interactions: 31616
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  29 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   SER A 259 "
            pdb=" OG  SER A 259 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ASP A 526 "
            pdb=" ND2 ASN A 529 "
     model   vdw
     2.384 3.120
  nonbonded pdb=" O   PRO A 402 "
            pdb=" NZ  LYS A 407 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" O   MET A 188 "
            pdb=" N   LEU A 190 "
     model   vdw
     2.400 3.120
  ... (remaining 31611 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.680
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
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      :  0.003   0.031   4029  Z= 0.171
  Angle     :  0.737   6.466   5487  Z= 0.464
  Chirality :  0.035   0.136    629
  Planarity :  0.004   0.041    680
  Dihedral  : 13.802  85.821   1416
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.67 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.37), residues: 492
  helix:  0.75 (0.24), residues: 386
  sheet:  None (None), residues: 0
  loop : -2.47 (0.69), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.010   0.001   PHE A 479 
 TYR   0.012   0.001   TYR A 324 
 ARG   0.003   0.000   ARG A 196 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6772 (tm-30)
REVERT: A  474 ILE cc_start: 0.8674 (mm) cc_final: 0.8357 (mm)
REVERT: A  552 LEU cc_start: 0.8554 (tp) cc_final: 0.8319 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1461
  time to fit residues: 28.0638
Evaluate side-chains
  109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0270
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0050
   overall best weight:    0.5652

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 565 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.180415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153390 restraints weight = 5264.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.157633 restraints weight = 2842.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.160406 restraints weight = 1929.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4029  Z= 0.196
  Angle     :  0.668  10.130   5487  Z= 0.327
  Chirality :  0.039   0.178    629
  Planarity :  0.005   0.038    680
  Dihedral  :  4.336  26.714    540
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.08 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.42 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.40), residues: 492
  helix:  1.78 (0.26), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.75 (0.71), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.024   0.001   PHE A 496 
 TYR   0.021   0.002   TYR A 481 
 ARG   0.004   0.001   ARG A 349 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.7762 (tpp) cc_final: 0.6961 (ttt)
REVERT: A  335 TYR cc_start: 0.8568 (m-10) cc_final: 0.8246 (m-10)
REVERT: A  552 LEU cc_start: 0.8634 (tp) cc_final: 0.8338 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 116
  average time/residue: 0.1255
  time to fit residues: 18.9489
Evaluate side-chains
  110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 330 GLN
A 332 GLN
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.175074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148510 restraints weight = 5363.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152726 restraints weight = 2874.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.155477 restraints weight = 1941.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4029  Z= 0.205
  Angle     :  0.635   9.672   5487  Z= 0.315
  Chirality :  0.040   0.199    629
  Planarity :  0.005   0.039    680
  Dihedral  :  4.253  24.601    540
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.28 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.29 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.40), residues: 492
  helix:  1.95 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -1.46 (0.75), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.020   0.001   PHE A 496 
 TYR   0.013   0.001   TYR A 324 
 ARG   0.003   0.000   ARG A 192 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8656 (t0) cc_final: 0.8437 (t0)
REVERT: A  326 MET cc_start: 0.8855 (ttp) cc_final: 0.8652 (ttp)
REVERT: A  328 TYR cc_start: 0.8954 (t80) cc_final: 0.8637 (t80)
REVERT: A  335 TYR cc_start: 0.8670 (m-10) cc_final: 0.8213 (m-10)
REVERT: A  369 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A  449 TYR cc_start: 0.7218 (m-80) cc_final: 0.6993 (m-80)
REVERT: A  552 LEU cc_start: 0.8585 (tp) cc_final: 0.8350 (tt)
REVERT: A  561 GLU cc_start: 0.8426 (tp30) cc_final: 0.8161 (tm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1157
  time to fit residues: 17.1108
Evaluate side-chains
  106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  275 CYS
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  428 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.174496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.146874 restraints weight = 5455.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.151092 restraints weight = 2981.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153911 restraints weight = 2046.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4029  Z= 0.195
  Angle     :  0.616   8.377   5487  Z= 0.306
  Chirality :  0.040   0.167    629
  Planarity :  0.005   0.037    680
  Dihedral  :  4.280  24.561    540
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.89 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 22.49 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.41), residues: 492
  helix:  2.11 (0.26), residues: 384
  sheet: -2.66 (1.28), residues: 10
  loop : -0.99 (0.83), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 341 
 PHE   0.023   0.001   PHE A 527 
 TYR   0.015   0.001   TYR A 560 
 ARG   0.004   0.000   ARG A  31 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8565 (tp) cc_final: 0.8317 (tp)
REVERT: A  185 ASP cc_start: 0.8754 (t0) cc_final: 0.8491 (t0)
REVERT: A  328 TYR cc_start: 0.8912 (t80) cc_final: 0.8402 (t80)
REVERT: A  335 TYR cc_start: 0.8620 (m-10) cc_final: 0.8205 (m-10)
REVERT: A  552 LEU cc_start: 0.8632 (tp) cc_final: 0.8395 (tt)
  outliers start: 17
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1218
  time to fit residues: 17.1505
Evaluate side-chains
  110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.171878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144028 restraints weight = 5591.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148265 restraints weight = 3023.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.151069 restraints weight = 2067.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4029  Z= 0.207
  Angle     :  0.617   7.637   5487  Z= 0.309
  Chirality :  0.041   0.161    629
  Planarity :  0.005   0.042    680
  Dihedral  :  4.210  21.470    540
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.10 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.73 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.41), residues: 492
  helix:  2.17 (0.26), residues: 384
  sheet: -2.00 (1.63), residues: 10
  loop : -0.80 (0.83), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  30 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.029   0.002   PHE A 527 
 TYR   0.012   0.001   TYR A 560 
 ARG   0.003   0.000   ARG A 192 

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASP cc_start: 0.8662 (t0) cc_final: 0.8305 (t0)
REVERT: A  328 TYR cc_start: 0.8915 (t80) cc_final: 0.8328 (t80)
REVERT: A  335 TYR cc_start: 0.8629 (m-10) cc_final: 0.8316 (m-10)
REVERT: A  481 TYR cc_start: 0.8886 (t80) cc_final: 0.8568 (t80)
REVERT: A  561 GLU cc_start: 0.8400 (tp30) cc_final: 0.8054 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1159
  time to fit residues: 16.7290
Evaluate side-chains
  107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 TRP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 TYR
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  459 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 67.1109 > 50:
  distance: 2 - 19:  21.514
  distance: 6 - 28:  32.628
  distance: 11 - 36:  26.005
  distance: 14 - 19:  24.896
  distance: 15 - 41:  28.870
  distance: 19 - 20:  27.996
  distance: 20 - 21:  24.202
  distance: 20 - 23:  45.104
  distance: 21 - 22:  33.931
  distance: 21 - 28:  18.384
  distance: 22 - 52:  27.773
  distance: 23 - 24:  41.832
  distance: 24 - 25:  61.872
  distance: 25 - 26:  32.796
  distance: 26 - 27:  26.280
  distance: 28 - 29:  31.650
  distance: 29 - 30:  32.350
  distance: 29 - 32:  53.575
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