Starting phenix.real_space_refine
on Mon Jun  9 17:08:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lxe_30006/06_2025/6lxe_30006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lxe_30006/06_2025/6lxe_30006.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lxe_30006/06_2025/6lxe_30006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lxe_30006/06_2025/6lxe_30006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lxe_30006/06_2025/6lxe_30006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lxe_30006/06_2025/6lxe_30006.cif"
  }
  resolution = 4.2
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5260 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      41      5.16       5
     C    4145      2.51       5
     N    1144      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6519
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 768, 6133
          Classifications: {'peptide': 768}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 41, 'TRANS': 726}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 197
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 205
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "C"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 179
          Classifications: {'peptide': 21}
          Link IDs: {'TRANS': 20}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    868  SG  CYS A 561      46.109  27.096  56.345  1.00175.10           S
  ATOM   1826  SG  CYS A 676      43.492  29.089  55.869  1.00148.02           S
  ATOM    676  SG  CYS A 536      30.126  51.769  48.423  1.00151.24           S
  ATOM    691  SG  CYS A 538      29.902  54.514  44.875  1.00154.18           S

  Time building chain proxies: 4.53, per 1000 atoms: 0.69
  Number of scatterers: 6519
  At special positions: 0
  Unit cell: (93.826, 117.828, 112.373, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      41     16.00
     O    1187      8.00
     N    1144      7.00
     C    4145      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: 1.52
  Conformation dependent library (CDL) restraints added in 845.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 676 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 609 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 680 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 561 "
      pdb="  ZN A1402 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 536 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1026 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A 549 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 538 "
      Number of angles added : 4


  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      49.0% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 438 through 452
      removed outlier: 4.940A  pdb=" N   LYS A 447 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   PHE A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 550
    Processing helix  chain 'A' and resid 641 through 654
    Processing helix  chain 'A' and resid 698 through 709
    Processing helix  chain 'A' and resid 719 through 726
      removed outlier: 4.292A  pdb=" N   GLU A 726 " --> pdb=" O   MET A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 736
    Processing helix  chain 'A' and resid 790 through 804
    Processing helix  chain 'A' and resid 811 through 829
      removed outlier: 4.114A  pdb=" N   LYS A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 4.199A  pdb=" N   CYS A 857 " --> pdb=" O   ARG A 853 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   MET A 861 " --> pdb=" O   CYS A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 876
      removed outlier: 4.439A  pdb=" N   VAL A 865 " --> pdb=" O   MET A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 890 through 897
      removed outlier: 3.834A  pdb=" N   GLN A 894 " --> pdb=" O   ARG A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 919
    Processing helix  chain 'A' and resid 965 through 988
      removed outlier: 3.861A  pdb=" N   ALA A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1005
      removed outlier: 3.515A  pdb=" N   GLN A1005 " --> pdb=" O   THR A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1014
      removed outlier: 3.757A  pdb=" N   LEU A1009 " --> pdb=" O   GLN A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1032 through 1055
      removed outlier: 3.626A  pdb=" N   GLY A1055 " --> pdb=" O   VAL A1051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1069
      removed outlier: 3.724A  pdb=" N   ALA A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1080
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1094 through 1098
    Processing helix  chain 'A' and resid 1104 through 1115
    Processing helix  chain 'A' and resid 1121 through 1128
    Processing helix  chain 'A' and resid 1145 through 1165
      removed outlier: 3.817A  pdb=" N   LEU A1149 " --> pdb=" O   ARG A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1180
    Processing helix  chain 'A' and resid 1183 through 1195
      removed outlier: 4.255A  pdb=" N   GLN A1187 " --> pdb=" O   ASN A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1232
    Processing helix  chain 'A' and resid 1233 through 1245
      removed outlier: 3.954A  pdb=" N   VAL A1237 " --> pdb=" O   ASP A1233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1255
      removed outlier: 3.547A  pdb=" N   PHE A1252 " --> pdb=" O   ARG A1248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 750
    Processing helix  chain 'C' and resid 730 through 747
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415
      removed outlier: 6.338A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 621
      removed outlier: 3.741A  pdb=" N   PHE A 604 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 740 through 742

    278 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2181
        1.34 -     1.46: 1457
        1.46 -     1.58: 2966
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 6669
  Sorted by residual:
  bond pdb=" C   VAL A 714 "
       pdb=" N   PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.015 1.11e-02 8.12e+03 1.94e+00
  bond pdb=" C   THR A 898 "
       pdb=" N   HIS A 899 "
    ideal  model  delta    sigma   weight residual
    1.331  1.306  0.025 2.07e-02 2.33e+03 1.40e+00
  bond pdb=" CB  PRO A 581 "
       pdb=" CG  PRO A 581 "
    ideal  model  delta    sigma   weight residual
    1.492  1.533 -0.041 5.00e-02 4.00e+02 6.81e-01
  bond pdb=" CA  ILE A 767 "
       pdb=" CB  ILE A 767 "
    ideal  model  delta    sigma   weight residual
    1.540  1.532  0.008 1.01e-02 9.80e+03 6.30e-01
  bond pdb=" N   ALA A 712 "
       pdb=" CA  ALA A 712 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.010 1.29e-02 6.01e+03 6.30e-01
  ... (remaining 6664 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 8708
        1.39 -     2.78: 260
        2.78 -     4.17: 40
        4.17 -     5.56: 19
        5.56 -     6.95: 2
  Bond angle restraints: 9029
  Sorted by residual:
  angle pdb=" C   ARG A 562 "
        pdb=" N   PRO A 563 "
        pdb=" CA  PRO A 563 "
      ideal   model   delta    sigma   weight residual
     118.85  122.90   -4.05 1.09e+00 8.42e-01 1.38e+01
  angle pdb=" N   CYS A 536 "
        pdb=" CA  CYS A 536 "
        pdb=" C   CYS A 536 "
      ideal   model   delta    sigma   weight residual
     108.20  113.11   -4.91 1.71e+00 3.42e-01 8.25e+00
  angle pdb=" C   LYS A 559 "
        pdb=" N   PRO A 560 "
        pdb=" CA  PRO A 560 "
      ideal   model   delta    sigma   weight residual
     119.84  122.83   -2.99 1.25e+00 6.40e-01 5.71e+00
  angle pdb=" C   HIS A 630 "
        pdb=" N   PHE A 631 "
        pdb=" CA  PHE A 631 "
      ideal   model   delta    sigma   weight residual
     121.54  126.00   -4.46 1.91e+00 2.74e-01 5.45e+00
  angle pdb=" CA  LEU C 735 "
        pdb=" CB  LEU C 735 "
        pdb=" CG  LEU C 735 "
      ideal   model   delta    sigma   weight residual
     116.30  123.25   -6.95 3.50e+00 8.16e-02 3.94e+00
  ... (remaining 9024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3600
       17.92 -    35.84: 347
       35.84 -    53.76: 63
       53.76 -    71.68: 13
       71.68 -    89.60: 9
  Dihedral angle restraints: 4032
    sinusoidal: 1643
      harmonic: 2389
  Sorted by residual:
  dihedral pdb=" CA  PRO A 779 "
           pdb=" C   PRO A 779 "
           pdb=" N   ALA A 780 "
           pdb=" CA  ALA A 780 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.89  -22.11     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  TRP A 848 "
           pdb=" C   TRP A 848 "
           pdb=" N   LYS A 849 "
           pdb=" CA  LYS A 849 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.78  -19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  PHE A 631 "
           pdb=" C   PHE A 631 "
           pdb=" N   ILE A 632 "
           pdb=" CA  ILE A 632 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.99  -16.01     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 500
       0.024 -    0.047: 289
       0.047 -    0.071: 128
       0.071 -    0.094: 50
       0.094 -    0.118: 25
  Chirality restraints: 992
  Sorted by residual:
  chirality pdb=" CA  ILE A 576 "
            pdb=" N   ILE A 576 "
            pdb=" C   ILE A 576 "
            pdb=" CB  ILE A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.46e-01
  chirality pdb=" CA  ILE A 592 "
            pdb=" N   ILE A 592 "
            pdb=" C   ILE A 592 "
            pdb=" CB  ILE A 592 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  chirality pdb=" CA  VAL A 742 "
            pdb=" N   VAL A 742 "
            pdb=" C   VAL A 742 "
            pdb=" CB  VAL A 742 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.26e-01
  ... (remaining 989 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 580 "    0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO A 581 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 579 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO A 580 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 580 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 580 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 579 "    0.006 2.00e-02 2.50e+03   1.12e-02 1.26e+00
        pdb=" C   SER A 579 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   SER A 579 "    0.007 2.00e-02 2.50e+03
        pdb=" N   PRO A 580 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 72
        2.60 -     3.18: 5710
        3.18 -     3.75: 10902
        3.75 -     4.33: 13621
        4.33 -     4.90: 21403
  Nonbonded interactions: 51708
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 433 "
            pdb=" CG2 THR A 565 "
     model   vdw
     2.030 3.460
  nonbonded pdb=" O   ARG A1213 "
            pdb=" OG1 THR A1216 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ARG A 914 "
            pdb=" OG  SER A 918 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   GLN A1096 "
            pdb=" OG1 THR A1100 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" N   GLY A 739 "
            pdb=" O   ILE A 754 "
     model   vdw
     2.253 3.120
  ... (remaining 51703 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 729 through 749)
  selection = chain 'C'
}

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:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.890
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
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      :  0.017   0.660   6677  Z= 0.474
  Angle     :  0.777  31.319   9033  Z= 0.346
  Chirality :  0.038   0.118    992
  Planarity :  0.003   0.043   1177
  Dihedral  : 15.295  89.603   2476
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  7.06 %
    Favored  : 92.80 %
  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: -3.22 (0.27), residues: 803
  helix: -0.83 (0.25), residues: 367
  sheet: -1.64 (0.87), residues: 39
  loop : -3.62 (0.27), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 848 
 HIS   0.004   0.001   HIS A 983 
 PHE   0.008   0.001   PHE A 970 
 TYR   0.006   0.001   TYR A1229 
 ARG   0.002   0.000   ARG A 684 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11001 (  278)
  hydrogen bonds       : angle       4.80294 (  810)
  metal coordination   : bond        0.47784 (    8)
  metal coordination   : angle      24.13672 (    4)
  covalent geometry    : bond        0.00232 ( 6669)
  covalent geometry    : angle       0.58840 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  861 MET cc_start: 0.7725 (mtm) cc_final: 0.7288 (mtt)
REVERT: A  872 TYR cc_start: 0.8182 (t80) cc_final: 0.7952 (t80)
REVERT: A  914 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8080 (tpt170)
REVERT: A 1011 MET cc_start: 0.9073 (ptm) cc_final: 0.8745 (ppp)
REVERT: A 1021 PHE cc_start: 0.8098 (m-80) cc_final: 0.7806 (m-80)
REVERT: A 1241 MET cc_start: 0.8061 (mmp) cc_final: 0.7487 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 151
  average time/residue: 0.2016
  time to fit residues: 39.7766
Evaluate side-chains
  101 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    0.1980
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A 531 ASN
A 630 HIS
** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 724 GLN
A 858 GLN
A 868 HIS
A 909 ASN
A 915 ASN
A 924 GLN
A1038 HIS
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1144 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.093618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.077923 restraints weight = 42214.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 16)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.078830 restraints weight = 34316.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.079715 restraints weight = 29795.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6677  Z= 0.126
  Angle     :  0.629   9.924   9033  Z= 0.307
  Chirality :  0.041   0.133    992
  Planarity :  0.005   0.055   1177
  Dihedral  :  4.278  22.310    884
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.33 %
    Favored  : 94.52 %
  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: -2.41 (0.29), residues: 803
  helix:  0.01 (0.27), residues: 370
  sheet: -1.43 (0.86), residues: 39
  loop : -3.38 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 848 
 HIS   0.011   0.001   HIS A 630 
 PHE   0.029   0.001   PHE A1224 
 TYR   0.010   0.001   TYR A 574 
 ARG   0.005   0.001   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  278)
  hydrogen bonds       : angle       4.39364 (  810)
  metal coordination   : bond        0.03458 (    8)
  metal coordination   : angle       5.91044 (    4)
  covalent geometry    : bond        0.00279 ( 6669)
  covalent geometry    : angle       0.61721 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  636 MET cc_start: 0.8120 (ppp) cc_final: 0.7914 (ppp)
REVERT: A  914 ARG cc_start: 0.8914 (ttm110) cc_final: 0.8314 (tpt170)
REVERT: A 1155 GLN cc_start: 0.5989 (mm110) cc_final: 0.5372 (tp40)
REVERT: A 1241 MET cc_start: 0.8302 (mmp) cc_final: 0.7797 (tpt)
REVERT: B  737 GLU cc_start: 0.9384 (mp0) cc_final: 0.9022 (mp0)
REVERT: B  739 MET cc_start: 0.8680 (mmp) cc_final: 0.8334 (mmt)
REVERT: C  739 MET cc_start: 0.7257 (tpt) cc_final: 0.6354 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1808
  time to fit residues: 31.9079
Evaluate side-chains
  103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 33 optimal weight:   40.0000
   chunk 14 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1169 HIS
** B 736 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 = 0.3999 r_free = 0.3999 target = 0.087015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.074359 restraints weight = 41841.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.075535 restraints weight = 32254.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.076418 restraints weight = 26401.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6677  Z= 0.184
  Angle     :  0.688  10.758   9033  Z= 0.341
  Chirality :  0.043   0.122    992
  Planarity :  0.005   0.052   1177
  Dihedral  :  4.685  25.148    884
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  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: -2.36 (0.29), residues: 803
  helix: -0.08 (0.26), residues: 380
  sheet: -1.34 (0.86), residues: 39
  loop : -3.29 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 848 
 HIS   0.008   0.002   HIS A 700 
 PHE   0.015   0.002   PHE A 679 
 TYR   0.021   0.002   TYR A1229 
 ARG   0.004   0.001   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  278)
  hydrogen bonds       : angle       4.69601 (  810)
  metal coordination   : bond        0.03367 (    8)
  metal coordination   : angle       6.06633 (    4)
  covalent geometry    : bond        0.00388 ( 6669)
  covalent geometry    : angle       0.67584 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 ASP cc_start: 0.9215 (m-30) cc_final: 0.9013 (m-30)
REVERT: A  530 MET cc_start: 0.7163 (tmm) cc_final: 0.6898 (tmm)
REVERT: A  606 MET cc_start: 0.7908 (mtp) cc_final: 0.7386 (mtp)
REVERT: A  914 ARG cc_start: 0.8873 (ttm110) cc_final: 0.8197 (tpt170)
REVERT: A 1124 LEU cc_start: 0.9286 (mp) cc_final: 0.8840 (mp)
REVERT: A 1155 GLN cc_start: 0.5727 (mm110) cc_final: 0.5155 (mm110)
REVERT: A 1241 MET cc_start: 0.8713 (mmp) cc_final: 0.8399 (mmm)
REVERT: B  737 GLU cc_start: 0.9258 (mp0) cc_final: 0.8865 (mp0)
REVERT: B  739 MET cc_start: 0.8546 (mmp) cc_final: 0.8189 (mmt)
REVERT: B  748 GLU cc_start: 0.8144 (pt0) cc_final: 0.7732 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2146
  time to fit residues: 37.2084
Evaluate side-chains
  90 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 32 optimal weight:    0.4980
   chunk 54 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 65 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 15 optimal weight:   40.0000
   chunk 44 optimal weight:    8.9990
   overall best weight:    4.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 GLN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 HIS
A1222 GLN
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.085077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.072880 restraints weight = 43872.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.074009 restraints weight = 33868.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.074864 restraints weight = 27701.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6677  Z= 0.207
  Angle     :  0.744  13.104   9033  Z= 0.372
  Chirality :  0.044   0.128    992
  Planarity :  0.005   0.056   1177
  Dihedral  :  5.166  25.423    884
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 23.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  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: -2.56 (0.29), residues: 803
  helix: -0.29 (0.26), residues: 377
  sheet: -1.66 (0.82), residues: 39
  loop : -3.29 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A1078 
 HIS   0.009   0.002   HIS A 630 
 PHE   0.032   0.002   PHE A1224 
 TYR   0.026   0.002   TYR A1229 
 ARG   0.007   0.001   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04141 (  278)
  hydrogen bonds       : angle       5.00721 (  810)
  metal coordination   : bond        0.03373 (    8)
  metal coordination   : angle       6.66627 (    4)
  covalent geometry    : bond        0.00443 ( 6669)
  covalent geometry    : angle       0.73113 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  862 MET cc_start: 0.8941 (mmt) cc_final: 0.8628 (mmt)
REVERT: A  891 CYS cc_start: 0.8825 (t) cc_final: 0.8463 (m)
REVERT: A  899 HIS cc_start: 0.7915 (t-170) cc_final: 0.7607 (t-170)
REVERT: A  914 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8133 (tpt170)
REVERT: A 1021 PHE cc_start: 0.7907 (m-80) cc_final: 0.7675 (m-10)
REVERT: A 1155 GLN cc_start: 0.5703 (mm110) cc_final: 0.5487 (tp40)
REVERT: A 1241 MET cc_start: 0.8967 (mmp) cc_final: 0.8370 (tpt)
REVERT: A 1242 ASN cc_start: 0.8404 (p0) cc_final: 0.8199 (p0)
REVERT: B  739 MET cc_start: 0.8373 (mmp) cc_final: 0.8037 (mmt)
REVERT: B  748 GLU cc_start: 0.8258 (pt0) cc_final: 0.7833 (pp20)
REVERT: C  739 MET cc_start: 0.7761 (tpt) cc_final: 0.6613 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1797
  time to fit residues: 29.5220
Evaluate side-chains
  85 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
A 761 GLN
A 832 ASN
A 845 GLN
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 GLN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 HIS
A1155 GLN
A1173 HIS
A1256 GLN
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.080793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.068352 restraints weight = 44317.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.069496 restraints weight = 33653.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.070330 restraints weight = 27531.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6677  Z= 0.244
  Angle     :  0.817  16.166   9033  Z= 0.411
  Chirality :  0.047   0.140    992
  Planarity :  0.006   0.063   1177
  Dihedral  :  5.659  26.554    884
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 27.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.20 %
    Favored  : 93.66 %
  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: -2.78 (0.28), residues: 803
  helix: -0.60 (0.26), residues: 373
  sheet: -1.80 (0.81), residues: 37
  loop : -3.22 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 662 
 HIS   0.009   0.002   HIS A1038 
 PHE   0.022   0.003   PHE A1224 
 TYR   0.025   0.003   TYR A1081 
 ARG   0.007   0.001   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04556 (  278)
  hydrogen bonds       : angle       5.32080 (  810)
  metal coordination   : bond        0.02957 (    8)
  metal coordination   : angle       8.76538 (    4)
  covalent geometry    : bond        0.00519 ( 6669)
  covalent geometry    : angle       0.79655 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 MET cc_start: 0.7566 (tmm) cc_final: 0.7322 (tmm)
REVERT: A  606 MET cc_start: 0.8326 (mtp) cc_final: 0.8084 (mtp)
REVERT: A  655 ASP cc_start: 0.8090 (m-30) cc_final: 0.7610 (m-30)
REVERT: A  862 MET cc_start: 0.8965 (mmt) cc_final: 0.8575 (mmt)
REVERT: A  877 MET cc_start: 0.8711 (ppp) cc_final: 0.8490 (tmm)
REVERT: A  891 CYS cc_start: 0.8917 (t) cc_final: 0.8576 (m)
REVERT: A  914 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8197 (tpt170)
REVERT: A 1124 LEU cc_start: 0.9322 (mp) cc_final: 0.8926 (mp)
REVERT: A 1128 PHE cc_start: 0.8722 (m-80) cc_final: 0.7955 (m-80)
REVERT: A 1242 ASN cc_start: 0.8409 (p0) cc_final: 0.8202 (p0)
REVERT: B  737 GLU cc_start: 0.9203 (mp0) cc_final: 0.8873 (mp0)
REVERT: B  739 MET cc_start: 0.8456 (mmp) cc_final: 0.8230 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1829
  time to fit residues: 27.5846
Evaluate side-chains
  83 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 37 optimal weight:   40.0000
   chunk 47 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 65 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 79 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0040
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 GLN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
A1045 GLN
** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.088116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.075255 restraints weight = 41498.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.076532 restraints weight = 31334.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.077535 restraints weight = 25219.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6677  Z= 0.127
  Angle     :  0.701   9.202   9033  Z= 0.344
  Chirality :  0.043   0.133    992
  Planarity :  0.004   0.057   1177
  Dihedral  :  5.091  24.571    884
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.03 %
    Favored  : 96.83 %
  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: -2.31 (0.29), residues: 803
  helix:  0.04 (0.27), residues: 378
  sheet: -1.51 (0.81), residues: 39
  loop : -3.31 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1078 
 HIS   0.007   0.001   HIS A 983 
 PHE   0.022   0.001   PHE A 631 
 TYR   0.013   0.002   TYR A 552 
 ARG   0.005   0.000   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03574 (  278)
  hydrogen bonds       : angle       4.67266 (  810)
  metal coordination   : bond        0.02945 (    8)
  metal coordination   : angle       5.09891 (    4)
  covalent geometry    : bond        0.00289 ( 6669)
  covalent geometry    : angle       0.69265 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 MET cc_start: 0.7394 (tmm) cc_final: 0.6886 (tmm)
REVERT: A  606 MET cc_start: 0.8477 (mtp) cc_final: 0.7694 (mtp)
REVERT: A  914 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8373 (tpt170)
REVERT: A 1155 GLN cc_start: 0.7672 (mp-120) cc_final: 0.7316 (tp-100)
REVERT: A 1241 MET cc_start: 0.8692 (mmp) cc_final: 0.8247 (tpt)
REVERT: B  739 MET cc_start: 0.8475 (mmp) cc_final: 0.8189 (mmt)
REVERT: B  748 GLU cc_start: 0.8147 (pt0) cc_final: 0.7769 (pp20)
REVERT: C  739 MET cc_start: 0.7226 (tpt) cc_final: 0.6807 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1967
  time to fit residues: 31.7153
Evaluate side-chains
  83 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 34 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 51 optimal weight:    0.2980
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    3.0588

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

Flipped N/Q/H residues before XYZ refinement:
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 HIS
A1256 GLN
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.085722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.073152 restraints weight = 41910.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.074314 restraints weight = 32059.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.075238 restraints weight = 26227.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6677  Z= 0.167
  Angle     :  0.729  10.776   9033  Z= 0.362
  Chirality :  0.044   0.132    992
  Planarity :  0.005   0.059   1177
  Dihedral  :  5.182  24.766    884
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 21.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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: -2.38 (0.29), residues: 803
  helix: -0.07 (0.27), residues: 380
  sheet: -1.57 (0.82), residues: 39
  loop : -3.30 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1078 
 HIS   0.006   0.001   HIS A 983 
 PHE   0.031   0.002   PHE A1224 
 TYR   0.022   0.002   TYR A1229 
 ARG   0.005   0.000   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  278)
  hydrogen bonds       : angle       4.94299 (  810)
  metal coordination   : bond        0.02627 (    8)
  metal coordination   : angle       5.83677 (    4)
  covalent geometry    : bond        0.00369 ( 6669)
  covalent geometry    : angle       0.71879 ( 9029)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 MET cc_start: 0.7659 (tmm) cc_final: 0.7273 (tmm)
REVERT: A  682 MET cc_start: 0.6838 (ttm) cc_final: 0.6535 (ttm)
REVERT: A  862 MET cc_start: 0.8871 (mmt) cc_final: 0.8593 (mmt)
REVERT: A  888 GLN cc_start: 0.9045 (tp40) cc_final: 0.8778 (tp-100)
REVERT: A  891 CYS cc_start: 0.8699 (t) cc_final: 0.8463 (m)
REVERT: A  914 ARG cc_start: 0.8854 (ttm110) cc_final: 0.8237 (tpt170)
REVERT: A 1241 MET cc_start: 0.8924 (mmp) cc_final: 0.8428 (tpt)
REVERT: B  737 GLU cc_start: 0.9110 (mp0) cc_final: 0.8831 (mp0)
REVERT: B  739 MET cc_start: 0.8467 (mmp) cc_final: 0.8192 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1805
  time to fit residues: 27.0161
Evaluate side-chains
  82 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 68.4179 > 50:
  distance: 38 - 64:  21.366
  distance: 43 - 47:   9.145
  distance: 44 - 72:  22.647
  distance: 47 - 48:  10.946
  distance: 48 - 49:  32.666
  distance: 48 - 51:  19.365
  distance: 49 - 50:  36.174
  distance: 49 - 55:  39.115
  distance: 50 - 77:  35.780
  distance: 51 - 52:  15.056
  distance: 52 - 53:  38.253
  distance: 52 - 54:  14.827
  distance: 55 - 56:  25.576
  distance: 56 - 57:  12.399
  distance: 56 - 59:  14.232
  distance: 57 - 58:  17.986
  distance: 57 - 64:   4.251
  distance: 59 - 60:  14.543
  distance: 60 - 61:  14.734
  distance: 61 - 62:  10.504
  distance: 61 - 63:   3.020
  distance: 64 - 65:  15.661
  distance: 65 - 66:  10.659
  distance: 65 - 68:   8.906
  distance: 66 - 67:  18.928
  distance: 66 - 72:  29.614
  distance: 68 - 69:  30.004
  distance: 69 - 70:   9.894
  distance: 69 - 71:  12.896
  distance: 72 - 73:  12.158
  distance: 73 - 74:  27.193
  distance: 73 - 76:  33.980
  distance: 74 - 75:  10.494
  distance: 74 - 77:  31.219
  distance: 77 - 78:  14.236
  distance: 78 - 79:  29.811
  distance: 78 - 81:  24.944
  distance: 79 - 80:  26.097
  distance: 79 - 85:  20.033
  distance: 81 - 82:  43.253
  distance: 82 - 83:  33.820
  distance: 83 - 84:  32.036
  distance: 85 - 86:  19.088
  distance: 86 - 87:   9.769
  distance: 86 - 89:  34.373
  distance: 87 - 88:  30.836
  distance: 87 - 92:  16.442
  distance: 89 - 90:   8.009
  distance: 89 - 91:  41.916
  distance: 92 - 93:  30.293
  distance: 93 - 94:  26.548
  distance: 93 - 96:  32.904
  distance: 94 - 95:  49.201
  distance: 94 - 102:  30.199
  distance: 96 - 97:  33.168
  distance: 97 - 98:   6.401
  distance: 97 - 99:  35.024
  distance: 98 - 100:  13.276
  distance: 99 - 101:   9.631
  distance: 100 - 101:  34.695
  distance: 102 - 103:  13.046
  distance: 102 - 108:   7.885
  distance: 103 - 104:  42.104
  distance: 103 - 106:  13.056
  distance: 104 - 105:  29.127
  distance: 104 - 109:  20.655
  distance: 106 - 107:  24.462
  distance: 107 - 108:  30.245
  distance: 109 - 110:  20.330
  distance: 110 - 111:  57.318
  distance: 110 - 113:  11.532
  distance: 111 - 112:  28.927
  distance: 111 - 115:  20.637
  distance: 113 - 114:   8.300
  distance: 115 - 116:  20.523
  distance: 116 - 117:   9.300
  distance: 116 - 119:  31.582
  distance: 117 - 118:  32.480
  distance: 117 - 125:  11.098
  distance: 119 - 120:  14.609
  distance: 120 - 121:  16.888
  distance: 120 - 122:  19.176
  distance: 121 - 123:  10.352
  distance: 122 - 124:   5.447
  distance: 123 - 124:  10.138