Starting phenix.real_space_refine
on Wed Mar  5 17:00:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zms_60255/03_2025/8zms_60255.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zms_60255/03_2025/8zms_60255.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zms_60255/03_2025/8zms_60255.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zms_60255/03_2025/8zms_60255.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zms_60255/03_2025/8zms_60255.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zms_60255/03_2025/8zms_60255.cif"
  }
  resolution = 3.7
  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=   0.001 sd=   0.020
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      17      5.16       5
     C    1940      2.51       5
     N     463      2.21       5
     O     500      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2920
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 2910
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 24, 'TRANS': 361}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'ACH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.31, per 1000 atoms: 1.13
  Number of scatterers: 2920
  At special positions: 0
  Unit cell: (70.55, 59.76, 83.83, 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      17     16.00
     O     500      8.00
     N     463      7.00
     C    1940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 403.7 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  716

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      88.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 54
      removed outlier: 3.608A  pdb=" N   VAL A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   VAL A  54 " --> pdb=" O   TYR A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 4.051A  pdb=" N   ILE A  61 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 149
      removed outlier: 3.577A  pdb=" N   ASN A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 151 through 171
      removed outlier: 3.749A  pdb=" N   PHE A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 201
      removed outlier: 4.660A  pdb=" N   THR A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   SER A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 238
      Proline residue:  A 229  - end of helix
      removed outlier: 4.174A  pdb=" N   LEU A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 264
      removed outlier: 3.849A  pdb=" N   PHE A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 307
      Proline residue:  A 304  - end of helix
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.676A  pdb=" N   TRP A 315 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 329
    Processing helix  chain 'A' and resid 331 through 334
      removed outlier: 3.580A  pdb=" N   ALA A 334 " --> pdb=" O   TRP A 331 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 331 through 334'
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 355 through 374
      removed outlier: 3.529A  pdb=" N   TYR A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL A 374 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'A' and resid 379 through 413
      removed outlier: 3.900A  pdb=" N   LEU A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      Proline residue:  A 403  - end of helix
    Processing helix  chain 'A' and resid 418 through 446
      removed outlier: 4.151A  pdb=" N   ALA A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      Proline residue:  A 436  - end of helix
      removed outlier: 4.386A  pdb=" N   GLY A 440 " --> pdb=" O   PRO A 436 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   HIS A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 463
    Processing helix  chain 'A' and resid 464 through 469
      removed outlier: 3.774A  pdb=" N   LEU A 467 " --> pdb=" O   PRO A 464 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 468 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 469 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 464 through 469'

    229 hydrogen bonds defined for protein.
    681 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.87

  Time building geometry restraints manager: 0.93 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.31: 450
        1.31 -     1.43: 765
        1.43 -     1.56: 1746
        1.56 -     1.68: 0
        1.68 -     1.81: 28
  Bond restraints: 2989
  Sorted by residual:
  bond pdb=" C5  ACH A1001 "
       pdb=" O4  ACH A1001 "
    ideal  model  delta    sigma   weight residual
    1.335  1.410 -0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb=" C2  ACH A1001 "
       pdb=" C3  ACH A1001 "
    ideal  model  delta    sigma   weight residual
    1.509  1.553 -0.044 2.00e-02 2.50e+03 4.86e+00
  bond pdb=" C5  ACH A1001 "
       pdb=" C6  ACH A1001 "
    ideal  model  delta    sigma   weight residual
    1.497  1.541 -0.044 2.00e-02 2.50e+03 4.82e+00
  bond pdb=" CA  VAL A 336 "
       pdb=" C   VAL A 336 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 8.80e-03 1.29e+04 3.04e+00
  bond pdb=" C   ILE A 303 "
       pdb=" N   PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.23e-02 6.61e+03 2.99e+00
  ... (remaining 2984 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 3867
        2.14 -     4.29: 157
        4.29 -     6.43: 37
        6.43 -     8.58: 17
        8.58 -    10.72: 4
  Bond angle restraints: 4082
  Sorted by residual:
  angle pdb=" C   PHE A 335 "
        pdb=" N   VAL A 336 "
        pdb=" CA  VAL A 336 "
      ideal   model   delta    sigma   weight residual
     120.24  123.54   -3.30 6.30e-01 2.52e+00 2.74e+01
  angle pdb=" N   PRO A 229 "
        pdb=" CA  PRO A 229 "
        pdb=" C   PRO A 229 "
      ideal   model   delta    sigma   weight residual
     110.70  115.83   -5.13 1.22e+00 6.72e-01 1.77e+01
  angle pdb=" CA  PRO A 229 "
        pdb=" C   PRO A 229 "
        pdb=" N   PRO A 230 "
      ideal   model   delta    sigma   weight residual
     117.93  122.77   -4.84 1.20e+00 6.94e-01 1.63e+01
  angle pdb=" N   VAL A 374 "
        pdb=" CA  VAL A 374 "
        pdb=" C   VAL A 374 "
      ideal   model   delta    sigma   weight residual
     108.88  116.63   -7.75 2.16e+00 2.14e-01 1.29e+01
  angle pdb=" C10 ACH A1001 "
        pdb=" N1  ACH A1001 "
        pdb=" C9  ACH A1001 "
      ideal   model   delta    sigma   weight residual
     108.54  119.26  -10.72 3.00e+00 1.11e-01 1.28e+01
  ... (remaining 4077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.28: 1595
       11.28 -    22.57: 128
       22.57 -    33.85: 26
       33.85 -    45.13: 10
       45.13 -    56.42: 3
  Dihedral angle restraints: 1762
    sinusoidal: 648
      harmonic: 1114
  Sorted by residual:
  dihedral pdb=" CA  SER A 379 "
           pdb=" C   SER A 379 "
           pdb=" N   PHE A 380 "
           pdb=" CA  PHE A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ASP A 288 "
           pdb=" C   ASP A 288 "
           pdb=" N   PRO A 289 "
           pdb=" CA  PRO A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.35  -17.65     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  GLU A 206 "
           pdb=" C   GLU A 206 "
           pdb=" N   GLU A 207 "
           pdb=" CA  GLU A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.46  -17.54     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 1759 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 341
       0.049 -    0.098: 113
       0.098 -    0.147: 36
       0.147 -    0.195: 6
       0.195 -    0.244: 1
  Chirality restraints: 497
  Sorted by residual:
  chirality pdb=" CB  VAL A  54 "
            pdb=" CA  VAL A  54 "
            pdb=" CG1 VAL A  54 "
            pdb=" CG2 VAL A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CG  LEU A 178 "
            pdb=" CB  LEU A 178 "
            pdb=" CD1 LEU A 178 "
            pdb=" CD2 LEU A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  ASN A 139 "
            pdb=" N   ASN A 139 "
            pdb=" C   ASN A 139 "
            pdb=" CB  ASN A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.30e-01
  ... (remaining 494 not shown)

  Planarity restraints: 501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 309 "    0.044 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 310 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 224 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.69e+00
        pdb=" C   GLY A 224 "    0.041 2.00e-02 2.50e+03
        pdb=" O   GLY A 224 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 225 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 228 "    0.037 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 229 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "    0.031 5.00e-02 4.00e+02
  ... (remaining 498 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 931
        2.86 -     3.37: 2895
        3.37 -     3.88: 4862
        3.88 -     4.39: 5087
        4.39 -     4.90: 8758
  Nonbonded interactions: 22533
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 127 "
            pdb=" OG  SER A 130 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   ASP A 174 "
            pdb=" OG1 THR A 177 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" OD2 ASP A 147 "
            pdb=" OG  SER A 419 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" ND2 ASN A 139 "
            pdb=" OD2 ASP A 425 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" O   GLN A 135 "
            pdb=" ND2 ASN A 139 "
     model   vdw
     2.412 3.120
  ... (remaining 22528 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:             3.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.560
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
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   0.075   2989  Z= 0.437
  Angle     :  1.147  10.721   4082  Z= 0.589
  Chirality :  0.055   0.244    497
  Planarity :  0.010   0.066    501
  Dihedral  :  9.676  56.418   1046
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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: -3.71 (0.32), residues: 380
  helix: -2.04 (0.21), residues: 301
  sheet:  None (None), residues: 0
  loop : -3.30 (0.64), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 325 
 HIS   0.005   0.001   HIS A 338 
 PHE   0.019   0.003   PHE A 238 
 TYR   0.014   0.002   TYR A  50 
 ARG   0.002   0.001   ARG A 378 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7771 (tt0) cc_final: 0.7280 (pm20)
REVERT: A  254 PHE cc_start: 0.7232 (t80) cc_final: 0.7026 (m-80)
REVERT: A  286 MET cc_start: 0.5604 (mmp) cc_final: 0.4183 (ttm)
REVERT: A  305 LEU cc_start: 0.8372 (mt) cc_final: 0.8097 (mt)
REVERT: A  429 SER cc_start: 0.8595 (m) cc_final: 0.8097 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1360
  time to fit residues: 14.9025
Evaluate side-chains
  65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   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 302 ASN
** A 338 HIS ** 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 = 0.4085 r_free = 0.4085 target = 0.180389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.164933 restraints weight = 4648.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.168713 restraints weight = 2485.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.171266 restraints weight = 1550.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2989  Z= 0.254
  Angle     :  0.740   7.238   4082  Z= 0.363
  Chirality :  0.042   0.136    497
  Planarity :  0.006   0.048    501
  Dihedral  :  5.862  47.277    415
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.75 %
    Favored  : 85.62 %
  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: -1.04 (0.41), residues: 380
  helix: -0.09 (0.28), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.34 (0.68), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 315 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.026   0.002   PHE A 169 
 TYR   0.011   0.002   TYR A 352 
 ARG   0.001   0.000   ARG A 470 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7737 (tt0) cc_final: 0.7348 (pm20)
REVERT: A  286 MET cc_start: 0.5651 (mmp) cc_final: 0.4164 (ttp)
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 0.0927
  time to fit residues: 8.9485
Evaluate side-chains
  65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.177118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.162010 restraints weight = 4581.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.165867 restraints weight = 2439.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168327 restraints weight = 1503.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2989  Z= 0.233
  Angle     :  0.701   7.103   4082  Z= 0.342
  Chirality :  0.041   0.118    497
  Planarity :  0.005   0.039    501
  Dihedral  :  5.481  42.320    415
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.38 %
    Favored  : 81.70 %
  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:  0.11 (0.44), residues: 380
  helix:  0.76 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -3.00 (0.67), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 325 
 HIS   0.002   0.000   HIS A 283 
 PHE   0.023   0.002   PHE A 169 
 TYR   0.009   0.001   TYR A 428 
 ARG   0.001   0.000   ARG A 470 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7709 (tt0) cc_final: 0.7338 (pm20)
REVERT: A  286 MET cc_start: 0.5654 (mmp) cc_final: 0.4159 (ttp)
REVERT: A  410 ASP cc_start: 0.8239 (m-30) cc_final: 0.7954 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 67
  average time/residue: 0.0807
  time to fit residues: 7.6064
Evaluate side-chains
  66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  372 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.178886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.164152 restraints weight = 4680.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.167822 restraints weight = 2540.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.170322 restraints weight = 1591.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2989  Z= 0.244
  Angle     :  0.690   6.970   4082  Z= 0.339
  Chirality :  0.041   0.131    497
  Planarity :  0.005   0.036    501
  Dihedral  :  5.385  43.280    415
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 15.69 %
    Favored  : 80.07 %
  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:  0.52 (0.45), residues: 380
  helix:  1.06 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -2.91 (0.69), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 357 
 HIS   0.002   0.001   HIS A 283 
 PHE   0.020   0.002   PHE A 169 
 TYR   0.011   0.002   TYR A 432 
 ARG   0.002   0.000   ARG A 470 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7688 (tt0) cc_final: 0.7386 (pm20)
REVERT: A  286 MET cc_start: 0.5773 (mmp) cc_final: 0.4246 (ttp)
REVERT: A  410 ASP cc_start: 0.8239 (m-30) cc_final: 0.7982 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0838
  time to fit residues: 8.0077
Evaluate side-chains
  69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.174323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.159450 restraints weight = 4670.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.163261 restraints weight = 2514.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.165761 restraints weight = 1559.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2989  Z= 0.276
  Angle     :  0.727   8.442   4082  Z= 0.353
  Chirality :  0.043   0.153    497
  Planarity :  0.005   0.036    501
  Dihedral  :  5.418  43.725    415
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 14.71 %
    Favored  : 81.05 %
  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:  0.59 (0.45), residues: 380
  helix:  1.02 (0.30), residues: 317
  sheet:  None (None), residues: 0
  loop : -2.70 (0.78), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 357 
 HIS   0.003   0.001   HIS A 283 
 PHE   0.018   0.002   PHE A 169 
 TYR   0.013   0.002   TYR A 432 
 ARG   0.002   0.000   ARG A 470 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7810 (tt0) cc_final: 0.7433 (pm20)
REVERT: A  286 MET cc_start: 0.5997 (mmp) cc_final: 0.4353 (ttp)
REVERT: A  410 ASP cc_start: 0.8282 (m-30) cc_final: 0.8013 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0795
  time to fit residues: 7.2555
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0870
   chunk 37 optimal weight:    0.0870
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   overall best weight:    0.2714

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.179890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.164579 restraints weight = 4671.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168585 restraints weight = 2473.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.171196 restraints weight = 1514.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2989  Z= 0.187
  Angle     :  0.671   9.811   4082  Z= 0.323
  Chirality :  0.040   0.149    497
  Planarity :  0.005   0.038    501
  Dihedral  :  5.143  41.262    415
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.67 %
    Favored  : 80.39 %
  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:  1.04 (0.46), residues: 380
  helix:  1.44 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.65 (0.78), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 357 
 HIS   0.002   0.000   HIS A 283 
 PHE   0.019   0.001   PHE A 169 
 TYR   0.009   0.001   TYR A 359 
 ARG   0.001   0.000   ARG A 378 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7746 (tt0) cc_final: 0.7406 (pm20)
REVERT: A  286 MET cc_start: 0.5880 (mmp) cc_final: 0.4284 (ttp)
REVERT: A  410 ASP cc_start: 0.8294 (m-30) cc_final: 0.7984 (m-30)
  outliers start: 9
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1010
  time to fit residues: 8.3713
Evaluate side-chains
  59 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0870
   chunk 23 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.179348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.163977 restraints weight = 4758.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.167915 restraints weight = 2512.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.170554 restraints weight = 1543.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2989  Z= 0.201
  Angle     :  0.687   8.691   4082  Z= 0.328
  Chirality :  0.041   0.128    497
  Planarity :  0.005   0.037    501
  Dihedral  :  5.088  39.917    415
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.65 %
    Favored  : 79.08 %
  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:  0.91 (0.45), residues: 380
  helix:  1.22 (0.30), residues: 317
  sheet:  None (None), residues: 0
  loop : -2.48 (0.82), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 357 
 HIS   0.002   0.000   HIS A 283 
 PHE   0.017   0.001   PHE A 169 
 TYR   0.009   0.001   TYR A 359 
 ARG   0.001   0.000   ARG A 470 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7768 (tt0) cc_final: 0.7430 (pm20)
REVERT: A  286 MET cc_start: 0.5934 (mmp) cc_final: 0.4275 (ttp)
REVERT: A  332 LEU cc_start: 0.8399 (tt) cc_final: 0.8108 (tp)
REVERT: A  410 ASP cc_start: 0.8407 (m-30) cc_final: 0.8095 (m-30)
  outliers start: 10
  outliers final: 5
  residues processed: 62
  average time/residue: 0.0870
  time to fit residues: 7.5061
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0470
   chunk 22 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.178657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.163699 restraints weight = 4624.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.167648 restraints weight = 2465.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.170119 restraints weight = 1505.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2989  Z= 0.211
  Angle     :  0.686   6.794   4082  Z= 0.330
  Chirality :  0.041   0.143    497
  Planarity :  0.005   0.037    501
  Dihedral  :  5.320  50.936    415
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.97 %
    Favored  : 80.07 %
  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:  0.92 (0.45), residues: 380
  helix:  1.21 (0.30), residues: 317
  sheet:  None (None), residues: 0
  loop : -2.38 (0.83), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 357 
 HIS   0.002   0.000   HIS A 283 
 PHE   0.015   0.001   PHE A 169 
 TYR   0.009   0.001   TYR A 359 
 ARG   0.001   0.000   ARG A 470 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7774 (tt0) cc_final: 0.7454 (pm20)
REVERT: A  286 MET cc_start: 0.5900 (mmp) cc_final: 0.4296 (ttp)
REVERT: A  316 MET cc_start: 0.7381 (mmt) cc_final: 0.7168 (mmt)
REVERT: A  332 LEU cc_start: 0.8367 (tt) cc_final: 0.8121 (tp)
REVERT: A  410 ASP cc_start: 0.8373 (m-30) cc_final: 0.8070 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0832
  time to fit residues: 7.0293
Evaluate side-chains
  61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.182768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.167432 restraints weight = 4609.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.171400 restraints weight = 2508.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.173948 restraints weight = 1555.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2989  Z= 0.211
  Angle     :  0.700   9.288   4082  Z= 0.336
  Chirality :  0.041   0.144    497
  Planarity :  0.005   0.036    501
  Dihedral  :  5.264  49.970    415
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.65 %
    Favored  : 80.39 %
  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:  0.86 (0.45), residues: 380
  helix:  1.19 (0.30), residues: 316
  sheet:  None (None), residues: 0
  loop : -2.45 (0.81), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 357 
 HIS   0.002   0.000   HIS A 283 
 PHE   0.014   0.001   PHE A 169 
 TYR   0.010   0.001   TYR A  50 
 ARG   0.001   0.000   ARG A 470 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7785 (tt0) cc_final: 0.7451 (pm20)
REVERT: A  286 MET cc_start: 0.5973 (mmp) cc_final: 0.4317 (ttp)
REVERT: A  316 MET cc_start: 0.7434 (mmt) cc_final: 0.7216 (mmt)
REVERT: A  332 LEU cc_start: 0.8380 (tt) cc_final: 0.8123 (tp)
REVERT: A  410 ASP cc_start: 0.8357 (m-30) cc_final: 0.8062 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0815
  time to fit residues: 6.8325
Evaluate side-chains
  59 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
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: 53.7364 > 50:
  distance: 15 - 20:  12.581
  distance: 20 - 21:  23.659
  distance: 21 - 22:  15.754
  distance: 22 - 23:  31.745
  distance: 22 - 24:  22.550
  distance: 24 - 25:  16.284
  distance: 25 - 26:  12.586
  distance: 25 - 28:  13.113
  distance: 26 - 27:  13.669
  distance: 26 - 31:  14.646
  distance: 28 - 29:  16.813
  distance: 28 - 30:  37.905
  distance: 31 - 32:   7.196
  distance: 31 - 37:   7.064
  distance: 32 - 33:   4.293
  distance: 32 - 35:  21.043
  distance: 33 - 38:   3.453
  distance: 35 - 36:   9.446
  distance: 36 - 37:  20.203
  distance: 38 - 39:   8.190
  distance: 39 - 40:   9.267
  distance: 39 - 42:   5.617
  distance: 40 - 41:  14.829
  distance: 40 - 46:  17.531
  distance: 42 - 43:   3.593
  distance: 42 - 44:   5.694
  distance: 43 - 45:   4.217
  distance: 47 - 48:   9.987
  distance: 47 - 50:  11.026
  distance: 48 - 49:  22.850
  distance: 48 - 56:  20.005
  distance: 50 - 51:   6.080
  distance: 51 - 52:  10.960
  distance: 51 - 53:   6.732
  distance: 52 - 54:   7.782
  distance: 53 - 55:   8.578
  distance: 54 - 55:   8.942
  distance: 56 - 57:   7.755
  distance: 57 - 58:  13.521
  distance: 57 - 60:  13.226
  distance: 58 - 59:  14.210
  distance: 58 - 67:  13.147
  distance: 60 - 61:  13.563
  distance: 61 - 62:   3.824
  distance: 62 - 63:   5.784
  distance: 63 - 64:   5.014
  distance: 64 - 65:   3.106
  distance: 67 - 68:  12.740
  distance: 68 - 69:   8.141
  distance: 68 - 71:  12.409
  distance: 69 - 70:  13.981
  distance: 69 - 75:  13.954
  distance: 71 - 72:   9.951
  distance: 72 - 73:   8.125
  distance: 72 - 74:   4.048
  distance: 75 - 76:   7.581
  distance: 76 - 77:   7.671
  distance: 76 - 79:   6.889
  distance: 77 - 78:   5.940
  distance: 77 - 83:   3.413
  distance: 79 - 80:   9.021
  distance: 80 - 81:  12.187
  distance: 81 - 82:  14.760
  distance: 83 - 84:   3.819
  distance: 84 - 85:  12.855
  distance: 84 - 87:  15.741
  distance: 85 - 86:  22.985
  distance: 85 - 91:  17.982
  distance: 87 - 88:  10.035
  distance: 88 - 89:  19.567
  distance: 88 - 90:  11.530
  distance: 91 - 92:  10.380
  distance: 92 - 93:  10.137
  distance: 92 - 95:  12.315
  distance: 93 - 94:   7.587
  distance: 93 - 99:   6.858
  distance: 94 - 117:  13.660
  distance: 95 - 96:  19.876
  distance: 96 - 97:  17.634
  distance: 96 - 98:  16.426