Starting phenix.real_space_refine
on Sun Jul 27 23:35:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6snh_10257/07_2025/6snh_10257.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6snh_10257/07_2025/6snh_10257.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6snh_10257/07_2025/6snh_10257.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6snh_10257/07_2025/6snh_10257.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6snh_10257/07_2025/6snh_10257.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6snh_10257/07_2025/6snh_10257.cif"
  }
  resolution = 3.9
  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=   0.002
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 3122 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      31      5.16       5
     C    4801      2.51       5
     N    1156      2.21       5
     O    1326      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7315
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "X"
      Number of atoms: 3924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 479, 3924
          Classifications: {'peptide': 479}
          Link IDs: {'PTRANS': 25, 'TRANS': 453}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1690
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 225, 1684
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213}
      Conformer: "B"
        Number of residues, atoms: 225, 1684
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213}
          bond proxies already assigned to first conformer: 1721
    Chain: "L"
      Number of atoms: 1659
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 214, 1641
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
      Conformer: "B"
        Number of residues, atoms: 214, 1641
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
          bond proxies already assigned to first conformer: 1654
    Chain: "X"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 42
          Unusual residues: {'LMH': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 6.21, per 1000 atoms: 0.85
  Number of scatterers: 7315
  At special positions: 0
  Unit cell: (110.04, 84.84, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P       1     15.00
     O    1326      8.00
     N    1156      7.00
     C    4801      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS X 314 " - pdb=" SG  CYS X 515 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 149 " - pdb=" SG  CYS H 205 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.05

  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: 2.26
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1736

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 9 sheets defined
      43.4% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'X' and resid 40 through 54
      removed outlier: 4.335A  pdb=" N   VAL X  47 " --> pdb=" O   PHE X  43 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 68 through 81
      removed outlier: 3.696A  pdb=" N   ALA X  72 " --> pdb=" O   GLY X  68 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLN X  81 " --> pdb=" O   MET X  77 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 84 through 88
      removed outlier: 3.657A  pdb=" N   TRP X  88 " --> pdb=" O   LEU X  85 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 101 through 119
      removed outlier: 3.824A  pdb=" N   ALA X 105 " --> pdb=" O   PRO X 101 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 120 through 124
      removed outlier: 3.823A  pdb=" N   ALA X 124 " --> pdb=" O   SER X 121 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 138 through 154
    Processing helix  chain 'X' and resid 154 through 170
      removed outlier: 3.521A  pdb=" N   VAL X 158 " --> pdb=" O   TYR X 154 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 172 through 185
      removed outlier: 4.045A  pdb=" N   ILE X 183 " --> pdb=" O   ALA X 179 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE X 185 " --> pdb=" O   SER X 181 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 186 through 194
    Processing helix  chain 'X' and resid 199 through 216
      removed outlier: 4.272A  pdb=" N   MET X 203 " --> pdb=" O   TYR X 199 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 218 through 233
      removed outlier: 3.818A  pdb=" N   VAL X 224 " --> pdb=" O   ALA X 220 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LYS X 233 " --> pdb=" O   SER X 229 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 234 through 238
      removed outlier: 3.862A  pdb=" N   TYR X 238 " --> pdb=" O   MET X 235 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 239 through 253
      removed outlier: 4.157A  pdb=" N   ALA X 245 " --> pdb=" O   PRO X 241 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 259 through 282
      removed outlier: 3.503A  pdb=" N   THR X 263 " --> pdb=" O   ILE X 259 " (cutoff:3.500A)
      Proline residue:  X 279  - end of helix
    Processing helix  chain 'X' and resid 286 through 298
    Processing helix  chain 'X' and resid 312 through 321
      removed outlier: 4.535A  pdb=" N   VAL X 318 " --> pdb=" O   CYS X 314 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   PHE X 319 " --> pdb=" O   VAL X 315 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 321 through 326
      removed outlier: 3.741A  pdb=" N   ARG X 325 " --> pdb=" O   LYS X 321 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 328 through 353
      removed outlier: 3.545A  pdb=" N   LEU X 336 " --> pdb=" O   GLN X 332 " (cutoff:3.500A)
      Proline residue:  X 345  - end of helix
    Processing helix  chain 'X' and resid 355 through 357
      No H-bonds generated for 'chain 'X' and resid 355 through 357'
    Processing helix  chain 'X' and resid 358 through 374
      removed outlier: 3.566A  pdb=" N   PHE X 373 " --> pdb=" O   SER X 369 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 382 through 391
      Proline residue:  X 388  - end of helix
    Processing helix  chain 'X' and resid 397 through 415
      removed outlier: 3.848A  pdb=" N   LEU X 401 " --> pdb=" O   ASP X 397 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU X 415 " --> pdb=" O   ALA X 411 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 415 through 421
    Processing helix  chain 'X' and resid 426 through 439
    Processing helix  chain 'X' and resid 476 through 499
      removed outlier: 3.730A  pdb=" N   PHE X 495 " --> pdb=" O   GLY X 491 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU X 496 " --> pdb=" O   PHE X 492 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP X 497 " --> pdb=" O   TYR X 493 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLN X 498 " --> pdb=" O   HIS X 494 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 509 through 536
      removed outlier: 3.742A  pdb=" N   PHE X 519 " --> pdb=" O   CYS X 515 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE X 520 " --> pdb=" O   ALA X 516 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   CYS X 521 " --> pdb=" O   VAL X 517 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 4.119A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 105
    Processing helix  chain 'H' and resid 195 through 199
    Processing helix  chain 'L' and resid 125 through 130
      removed outlier: 3.572A  pdb=" N   GLY L 130 " --> pdb=" O   GLN L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 191
      removed outlier: 3.700A  pdb=" N   HIS L 191 " --> pdb=" O   ASP L 187 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.666A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 129 through 133
      removed outlier: 4.278A  pdb=" N   SER H 188 " --> pdb=" O   PHE H 175 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE H 175 " --> pdb=" O   SER H 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 163
    Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.367A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.367A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 116 through 120
      removed outlier: 6.080A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 146 through 152

    366 hydrogen bonds defined for protein.
    1021 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: 2.06

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1506
        1.33 -     1.46: 2404
        1.46 -     1.58: 3589
        1.58 -     1.71: 2
        1.71 -     1.84: 44
  Bond restraints: 7545
  Sorted by residual:
  bond pdb=" C   SER L  10 "
       pdb=" O   SER L  10 "
    ideal  model  delta    sigma   weight residual
    1.235  1.344 -0.109 1.18e-02 7.18e+03 8.52e+01
  bond pdb=" C31 LMH X 601 "
       pdb=" O32 LMH X 601 "
    ideal  model  delta    sigma   weight residual
    1.418  1.500 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" C   SER L  10 "
       pdb=" CA ASER L  10 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 1.12e-02 7.97e+03 1.15e+01
  bond pdb=" C   SER L  10 "
       pdb=" CA BSER L  10 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 1.12e-02 7.97e+03 1.15e+01
  bond pdb=" N   VAL X 309 "
       pdb=" CA  VAL X 309 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.14e+01
  ... (remaining 7540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.40: 10171
        3.40 -     6.79: 100
        6.79 -    10.19: 12
       10.19 -    13.59: 4
       13.59 -    16.99: 5
  Bond angle restraints: 10292
  Sorted by residual:
  angle pdb=" CA  SER H 188 "
        pdb=" C   SER H 188 "
        pdb=" O   SER H 188 "
      ideal   model   delta    sigma   weight residual
     120.89  131.05  -10.16 1.10e+00 8.26e-01 8.53e+01
  angle pdb=" N   SER L  10 "
        pdb=" CA ASER L  10 "
        pdb=" C   SER L  10 "
      ideal   model   delta    sigma   weight residual
     108.13  123.32  -15.19 1.72e+00 3.38e-01 7.80e+01
  angle pdb=" N   SER L  10 "
        pdb=" CA BSER L  10 "
        pdb=" C   SER L  10 "
      ideal   model   delta    sigma   weight residual
     108.13  123.32  -15.19 1.72e+00 3.38e-01 7.80e+01
  angle pdb=" N   SER H 188 "
        pdb=" CA  SER H 188 "
        pdb=" C   SER H 188 "
      ideal   model   delta    sigma   weight residual
     108.76  122.69  -13.93 1.58e+00 4.01e-01 7.77e+01
  angle pdb=" O   SER L  10 "
        pdb=" C   SER L  10 "
        pdb=" CA ASER L  10 "
      ideal   model   delta    sigma   weight residual
     120.11  131.19  -11.08 1.37e+00 5.33e-01 6.54e+01
  ... (remaining 10287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 3951
       17.28 -    34.56: 371
       34.56 -    51.84: 74
       51.84 -    69.12: 21
       69.12 -    86.40: 6
  Dihedral angle restraints: 4423
    sinusoidal: 1700
      harmonic: 2723
  Sorted by residual:
  dihedral pdb=" N   HIS X 378 "
           pdb=" C   HIS X 378 "
           pdb=" CA  HIS X 378 "
           pdb=" CB  HIS X 378 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  149.53  -26.73     0      2.50e+00 1.60e-01 1.14e+02
  dihedral pdb=" C   HIS X 378 "
           pdb=" N   HIS X 378 "
           pdb=" CA  HIS X 378 "
           pdb=" CB  HIS X 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -149.26   26.66     0      2.50e+00 1.60e-01 1.14e+02
  dihedral pdb=" CB  CYS X 314 "
           pdb=" SG  CYS X 314 "
           pdb=" SG  CYS X 515 "
           pdb=" CB  CYS X 515 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.31   67.31     1      1.00e+01 1.00e-02 5.90e+01
  ... (remaining 4420 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.218: 1137
       0.218 -    0.435: 1
       0.435 -    0.653: 2
       0.653 -    0.871: 0
       0.871 -    1.088: 1
  Chirality restraints: 1141
  Sorted by residual:
  chirality pdb=" CA  HIS X 378 "
            pdb=" N   HIS X 378 "
            pdb=" C   HIS X 378 "
            pdb=" CB  HIS X 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.42    1.09 2.00e-01 2.50e+01 2.96e+01
  chirality pdb=" CA ASER L  10 "
            pdb=" N   SER L  10 "
            pdb=" C   SER L  10 "
            pdb=" CB ASER L  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CA BSER L  10 "
            pdb=" N   SER L  10 "
            pdb=" C   SER L  10 "
            pdb=" CB BSER L  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 4.99e+00
  ... (remaining 1138 not shown)

  Planarity restraints: 1267
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE X 384 "    0.046 5.00e-02 4.00e+02   7.02e-02 7.90e+00
        pdb=" N   PRO X 385 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO X 385 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO X 385 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L 165 "    0.013 2.00e-02 2.50e+03   2.47e-02 6.11e+00
        pdb=" C   VAL L 165 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   VAL L 165 "    0.016 2.00e-02 2.50e+03
        pdb=" N   THR L 166 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H 160 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.92e+00
        pdb=" C   THR H 160 "    0.042 2.00e-02 2.50e+03
        pdb=" O   THR H 160 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL H 161 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1264 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 648
        2.72 -     3.27: 8096
        3.27 -     3.81: 11907
        3.81 -     4.36: 14169
        4.36 -     4.90: 24151
  Nonbonded interactions: 58971
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG L 110 "
            pdb=" O   THR L 111 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" N   VAL H   2 "
            pdb=" O   SER H  25 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   HIS L 191 "
            pdb=" NH1 ARG L 213 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OH  TYR H  59 "
            pdb=" N   ILE H  69 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   TYR L 188 "
            pdb=" OH  TYR L 194 "
     model   vdw
     2.236 3.040
  ... (remaining 58966 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.30 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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.920
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
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      :  0.008   0.109   7550  Z= 0.433
  Angle     :  0.995  16.985  10302  Z= 0.568
  Chirality :  0.063   1.088   1141
  Planarity :  0.005   0.070   1267
  Dihedral  : 14.505  86.399   2672
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 19.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.99 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  5.96 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -4.30 (0.23), residues: 918
  helix: -1.92 (0.24), residues: 352
  sheet: -2.67 (0.29), residues: 202
  loop : -3.80 (0.26), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 163 
 HIS   0.006   0.001   HIS X 194 
 PHE   0.024   0.002   PHE X 197 
 TYR   0.021   0.002   TYR X 239 
 ARG   0.002   0.000   ARG H  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14030 (  355)
  hydrogen bonds       : angle       7.29690 ( 1021)
  SS BOND              : bond        0.00949 (    5)
  SS BOND              : angle       1.55663 (   10)
  covalent geometry    : bond        0.00815 ( 7545)
  covalent geometry    : angle       0.99445 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.640 
Fit side-chains
REVERT: X  189 LEU cc_start: 0.9340 (tp) cc_final: 0.9071 (tp)
REVERT: X  190 MET cc_start: 0.8352 (ttm) cc_final: 0.7928 (ttm)
REVERT: X  368 MET cc_start: 0.8839 (tpp) cc_final: 0.8632 (tpt)
REVERT: X  490 MET cc_start: 0.8787 (mtm) cc_final: 0.8280 (mtm)
REVERT: X  519 PHE cc_start: 0.8964 (t80) cc_final: 0.8626 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 67
  average time/residue: 0.3102
  time to fit residues: 29.3054
Evaluate side-chains
  44 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  380 LYS
Chi-restraints excluded: chain H residue  136 SER
Chi-restraints excluded: chain H residue  138 LYS
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue  166 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 81 optimal weight:    8.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
X  82 HIS
** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 289 ASN
X 291 HIS
X 295 HIS
X 408 ASN
X 441 ASN
H  13 GLN
H 180 GLN
L  37 GLN
L 191 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.061048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.047500 restraints weight = 84132.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.049492 restraints weight = 32443.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.050858 restraints weight = 18362.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7550  Z= 0.131
  Angle     :  0.632   7.460  10302  Z= 0.325
  Chirality :  0.043   0.173   1141
  Planarity :  0.005   0.050   1267
  Dihedral  :  7.567  88.624   1071
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.30 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.27), residues: 918
  helix:  0.06 (0.28), residues: 355
  sheet: -1.67 (0.34), residues: 177
  loop : -2.71 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP X 416 
 HIS   0.004   0.001   HIS X  82 
 PHE   0.018   0.001   PHE X 343 
 TYR   0.013   0.001   TYR X 239 
 ARG   0.003   0.000   ARG L 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  355)
  hydrogen bonds       : angle       5.62192 ( 1021)
  SS BOND              : bond        0.00875 (    5)
  SS BOND              : angle       1.25406 (   10)
  covalent geometry    : bond        0.00290 ( 7545)
  covalent geometry    : angle       0.63151 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 1.067 
Fit side-chains
REVERT: X  190 MET cc_start: 0.8781 (ttm) cc_final: 0.8568 (ttm)
REVERT: X  193 ASP cc_start: 0.8721 (m-30) cc_final: 0.8356 (m-30)
REVERT: X  490 MET cc_start: 0.8830 (mtm) cc_final: 0.8469 (mtm)
REVERT: L  140 ASN cc_start: 0.9211 (m-40) cc_final: 0.8879 (m-40)
REVERT: L  145 GLU cc_start: 0.9348 (tp30) cc_final: 0.9070 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.1903
  time to fit residues: 19.1807
Evaluate side-chains
  49 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  138 LYS
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  196 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 258 ASN ** 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 = 0.3261 r_free = 0.3261 target = 0.061074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.047402 restraints weight = 88679.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.049444 restraints weight = 33176.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.050879 restraints weight = 18538.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7550  Z= 0.135
  Angle     :  0.593   7.208  10302  Z= 0.302
  Chirality :  0.042   0.172   1141
  Planarity :  0.004   0.044   1267
  Dihedral  :  6.851  73.031   1064
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.78 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -1.42 (0.28), residues: 918
  helix:  0.66 (0.29), residues: 356
  sheet: -1.26 (0.34), residues: 177
  loop : -2.36 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 163 
 HIS   0.004   0.001   HIS X 357 
 PHE   0.017   0.001   PHE X 343 
 TYR   0.012   0.001   TYR H  94 
 ARG   0.002   0.000   ARG L 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03871 (  355)
  hydrogen bonds       : angle       5.30300 ( 1021)
  SS BOND              : bond        0.00610 (    5)
  SS BOND              : angle       0.93858 (   10)
  covalent geometry    : bond        0.00313 ( 7545)
  covalent geometry    : angle       0.59238 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.758 
Fit side-chains
REVERT: X  189 LEU cc_start: 0.9169 (tt) cc_final: 0.8849 (tt)
REVERT: X  190 MET cc_start: 0.8812 (ttm) cc_final: 0.8362 (ttm)
REVERT: X  490 MET cc_start: 0.8782 (mtm) cc_final: 0.8469 (mtm)
REVERT: X  519 PHE cc_start: 0.9278 (t80) cc_final: 0.8931 (t80)
REVERT: L  140 ASN cc_start: 0.9136 (m-40) cc_final: 0.8371 (m-40)
REVERT: L  145 GLU cc_start: 0.9293 (tp30) cc_final: 0.9027 (tp30)
  outliers start: 13
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1376
  time to fit residues: 12.3111
Evaluate side-chains
  51 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  368 MET
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  196 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
X 194 HIS
** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 258 ASN
X 408 ASN
X 409 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.060550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.046752 restraints weight = 95829.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.048761 restraints weight = 34346.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.050226 restraints weight = 19058.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7550  Z= 0.176
  Angle     :  0.597   6.033  10302  Z= 0.306
  Chirality :  0.042   0.167   1141
  Planarity :  0.004   0.045   1267
  Dihedral  :  6.855  71.029   1060
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.02 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -1.16 (0.28), residues: 918
  helix:  0.79 (0.28), residues: 356
  sheet: -0.94 (0.35), residues: 177
  loop : -2.21 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 163 
 HIS   0.003   0.001   HIS X 194 
 PHE   0.018   0.001   PHE X 343 
 TYR   0.015   0.001   TYR H  94 
 ARG   0.001   0.000   ARG X 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  355)
  hydrogen bonds       : angle       5.29528 ( 1021)
  SS BOND              : bond        0.00771 (    5)
  SS BOND              : angle       1.57942 (   10)
  covalent geometry    : bond        0.00406 ( 7545)
  covalent geometry    : angle       0.59520 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 1.972 
Fit side-chains
REVERT: X  190 MET cc_start: 0.8793 (ttm) cc_final: 0.8436 (ttm)
REVERT: X  408 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8397 (t0)
REVERT: X  490 MET cc_start: 0.8787 (mtm) cc_final: 0.8499 (mtm)
REVERT: L  140 ASN cc_start: 0.9119 (m-40) cc_final: 0.8327 (m-40)
REVERT: L  145 GLU cc_start: 0.9260 (tp30) cc_final: 0.9003 (tp30)
  outliers start: 19
  outliers final: 14
  residues processed: 60
  average time/residue: 0.2248
  time to fit residues: 21.1305
Evaluate side-chains
  63 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 1.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  242 ILE
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  408 ASN
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain L residue  137 LEU
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 81 optimal weight:    0.2980
   chunk 71 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
X 408 ASN
X 409 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.062336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.049072 restraints weight = 76855.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.051047 restraints weight = 30472.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.052457 restraints weight = 17364.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7550  Z= 0.109
  Angle     :  0.560   6.924  10302  Z= 0.283
  Chirality :  0.041   0.158   1141
  Planarity :  0.004   0.043   1267
  Dihedral  :  6.392  63.210   1060
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.76 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.69 (0.28), residues: 918
  helix:  1.15 (0.28), residues: 357
  sheet: -0.52 (0.36), residues: 182
  loop : -2.04 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X 416 
 HIS   0.003   0.001   HIS X  75 
 PHE   0.018   0.001   PHE X 343 
 TYR   0.010   0.001   TYR H  94 
 ARG   0.001   0.000   ARG L 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  355)
  hydrogen bonds       : angle       4.98863 ( 1021)
  SS BOND              : bond        0.00545 (    5)
  SS BOND              : angle       0.71792 (   10)
  covalent geometry    : bond        0.00245 ( 7545)
  covalent geometry    : angle       0.55993 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 2.394 
Fit side-chains
   revert: symmetry clash
REVERT: X  189 LEU cc_start: 0.9163 (tt) cc_final: 0.8740 (mt)
REVERT: X  190 MET cc_start: 0.8838 (ttm) cc_final: 0.8590 (ttm)
REVERT: X  490 MET cc_start: 0.8593 (mtm) cc_final: 0.8275 (mtm)
REVERT: X  519 PHE cc_start: 0.9208 (t80) cc_final: 0.8862 (t80)
REVERT: L  140 ASN cc_start: 0.8968 (m-40) cc_final: 0.8229 (m-40)
REVERT: L  145 GLU cc_start: 0.9246 (tp30) cc_final: 0.8997 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 73
  average time/residue: 0.2802
  time to fit residues: 30.6449
Evaluate side-chains
  65 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 2.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  242 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 89 optimal weight:    9.9990
   chunk 51 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 2 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3266 r_free = 0.3266 target = 0.061453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.048210 restraints weight = 79518.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.050175 restraints weight = 30781.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.051581 restraints weight = 17451.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7550  Z= 0.128
  Angle     :  0.575   6.279  10302  Z= 0.290
  Chirality :  0.041   0.176   1141
  Planarity :  0.004   0.044   1267
  Dihedral  :  6.420  62.280   1060
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.38 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.53 (0.28), residues: 918
  helix:  1.16 (0.28), residues: 358
  sheet: -0.20 (0.37), residues: 181
  loop : -1.96 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 163 
 HIS   0.002   0.001   HIS X  75 
 PHE   0.018   0.001   PHE X 343 
 TYR   0.012   0.001   TYR H  94 
 ARG   0.001   0.000   ARG X  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  355)
  hydrogen bonds       : angle       5.01523 ( 1021)
  SS BOND              : bond        0.00698 (    5)
  SS BOND              : angle       1.89989 (   10)
  covalent geometry    : bond        0.00298 ( 7545)
  covalent geometry    : angle       0.57190 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.748 
Fit side-chains
REVERT: X   77 MET cc_start: 0.8746 (mmm) cc_final: 0.8501 (mmm)
REVERT: X  189 LEU cc_start: 0.9064 (tt) cc_final: 0.8825 (mt)
REVERT: X  190 MET cc_start: 0.8885 (ttm) cc_final: 0.8604 (ttm)
REVERT: X  490 MET cc_start: 0.8638 (mtm) cc_final: 0.8303 (mtm)
REVERT: L  140 ASN cc_start: 0.9014 (m-40) cc_final: 0.8343 (m-40)
REVERT: L  145 GLU cc_start: 0.9253 (tp30) cc_final: 0.9011 (tp30)
  outliers start: 17
  outliers final: 14
  residues processed: 65
  average time/residue: 0.1343
  time to fit residues: 13.6376
Evaluate side-chains
  66 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  242 ILE
Chi-restraints excluded: chain X residue  368 MET
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3276 r_free = 0.3276 target = 0.061640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.047990 restraints weight = 122748.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.050841 restraints weight = 38253.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.051870 restraints weight = 17361.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7550  Z= 0.123
  Angle     :  0.575   8.525  10302  Z= 0.290
  Chirality :  0.041   0.170   1141
  Planarity :  0.004   0.045   1267
  Dihedral  :  6.387  61.045   1060
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.25 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.41 (0.29), residues: 918
  helix:  1.29 (0.29), residues: 356
  sheet: -0.13 (0.38), residues: 181
  loop : -1.92 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X 416 
 HIS   0.002   0.001   HIS X  75 
 PHE   0.017   0.001   PHE X 343 
 TYR   0.013   0.001   TYR H 103 
 ARG   0.001   0.000   ARG X  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  355)
  hydrogen bonds       : angle       4.92571 ( 1021)
  SS BOND              : bond        0.00708 (    5)
  SS BOND              : angle       0.79683 (   10)
  covalent geometry    : bond        0.00286 ( 7545)
  covalent geometry    : angle       0.57499 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.777 
Fit side-chains
REVERT: X   77 MET cc_start: 0.8733 (mmm) cc_final: 0.8421 (mmm)
REVERT: X  189 LEU cc_start: 0.9055 (tt) cc_final: 0.8851 (mt)
REVERT: X  190 MET cc_start: 0.8864 (ttm) cc_final: 0.8606 (ttm)
REVERT: X  490 MET cc_start: 0.8688 (mtm) cc_final: 0.8335 (mtm)
REVERT: X  519 PHE cc_start: 0.9191 (t80) cc_final: 0.8839 (t80)
REVERT: L  140 ASN cc_start: 0.9000 (m-40) cc_final: 0.8352 (m-40)
REVERT: L  145 GLU cc_start: 0.9302 (tp30) cc_final: 0.9059 (tp30)
  outliers start: 15
  outliers final: 14
  residues processed: 64
  average time/residue: 0.1304
  time to fit residues: 13.2101
Evaluate side-chains
  65 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  368 MET
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3292 r_free = 0.3292 target = 0.062368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.048924 restraints weight = 82749.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.050987 restraints weight = 31765.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.052409 restraints weight = 17884.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7550  Z= 0.106
  Angle     :  0.574   7.539  10302  Z= 0.286
  Chirality :  0.041   0.166   1141
  Planarity :  0.004   0.045   1267
  Dihedral  :  6.274  61.277   1060
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.13 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.30 (0.29), residues: 918
  helix:  1.40 (0.29), residues: 355
  sheet: -0.06 (0.38), residues: 181
  loop : -1.87 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 163 
 HIS   0.003   0.001   HIS X  75 
 PHE   0.018   0.001   PHE X 343 
 TYR   0.011   0.001   TYR H 103 
 ARG   0.001   0.000   ARG X  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03365 (  355)
  hydrogen bonds       : angle       4.86329 ( 1021)
  SS BOND              : bond        0.00523 (    5)
  SS BOND              : angle       1.38760 (   10)
  covalent geometry    : bond        0.00243 ( 7545)
  covalent geometry    : angle       0.57308 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.860 
Fit side-chains
REVERT: X  490 MET cc_start: 0.8564 (mtm) cc_final: 0.8276 (mtm)
REVERT: X  519 PHE cc_start: 0.9219 (t80) cc_final: 0.8828 (t80)
REVERT: L  140 ASN cc_start: 0.8940 (m-40) cc_final: 0.8242 (m-40)
REVERT: L  145 GLU cc_start: 0.9285 (tp30) cc_final: 0.9056 (tp30)
  outliers start: 18
  outliers final: 16
  residues processed: 70
  average time/residue: 0.1376
  time to fit residues: 15.1569
Evaluate side-chains
  69 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  140 THR
Chi-restraints excluded: chain X residue  242 ILE
Chi-restraints excluded: chain X residue  368 MET
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.061631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.047968 restraints weight = 97666.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.050058 restraints weight = 33843.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.051554 restraints weight = 18504.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7550  Z= 0.159
  Angle     :  0.633  12.451  10302  Z= 0.314
  Chirality :  0.042   0.172   1141
  Planarity :  0.004   0.046   1267
  Dihedral  :  6.560  62.213   1060
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.87 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.36 (0.29), residues: 918
  helix:  1.32 (0.29), residues: 354
  sheet: -0.09 (0.38), residues: 181
  loop : -1.87 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 163 
 HIS   0.002   0.001   HIS X  75 
 PHE   0.019   0.001   PHE X 343 
 TYR   0.015   0.001   TYR H  94 
 ARG   0.003   0.000   ARG X  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  355)
  hydrogen bonds       : angle       5.00060 ( 1021)
  SS BOND              : bond        0.00621 (    5)
  SS BOND              : angle       1.88430 (   10)
  covalent geometry    : bond        0.00368 ( 7545)
  covalent geometry    : angle       0.63097 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.788 
Fit side-chains
REVERT: X  490 MET cc_start: 0.8629 (mtm) cc_final: 0.8289 (mtm)
REVERT: X  519 PHE cc_start: 0.9262 (t80) cc_final: 0.8860 (t80)
REVERT: L  140 ASN cc_start: 0.8998 (m-40) cc_final: 0.8356 (m-40)
REVERT: L  145 GLU cc_start: 0.9213 (tp30) cc_final: 0.8993 (tp30)
  outliers start: 17
  outliers final: 16
  residues processed: 66
  average time/residue: 0.1403
  time to fit residues: 14.7832
Evaluate side-chains
  69 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  140 THR
Chi-restraints excluded: chain X residue  242 ILE
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0000
   chunk 70 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    1.0788

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.062706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.049180 restraints weight = 87293.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.051302 restraints weight = 32292.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.052772 restraints weight = 17774.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7550  Z= 0.114
  Angle     :  0.604  12.117  10302  Z= 0.296
  Chirality :  0.042   0.165   1141
  Planarity :  0.004   0.045   1267
  Dihedral  :  6.390  61.805   1060
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.63 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.29 (0.29), residues: 918
  helix:  1.38 (0.29), residues: 355
  sheet:  0.00 (0.38), residues: 175
  loop : -1.83 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X 416 
 HIS   0.003   0.001   HIS X  75 
 PHE   0.018   0.001   PHE X 343 
 TYR   0.011   0.001   TYR H  94 
 ARG   0.002   0.000   ARG X  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  355)
  hydrogen bonds       : angle       4.89319 ( 1021)
  SS BOND              : bond        0.00534 (    5)
  SS BOND              : angle       1.66974 (   10)
  covalent geometry    : bond        0.00265 ( 7545)
  covalent geometry    : angle       0.60157 (10292)

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

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

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1836 Ramachandran restraints generated.
    918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.783 
Fit side-chains
REVERT: X  490 MET cc_start: 0.8553 (mtm) cc_final: 0.8301 (mtm)
REVERT: L  140 ASN cc_start: 0.8917 (m-40) cc_final: 0.8229 (m-40)
REVERT: L  145 GLU cc_start: 0.9209 (tp30) cc_final: 0.8992 (tp30)
  outliers start: 16
  outliers final: 15
  residues processed: 68
  average time/residue: 0.1329
  time to fit residues: 14.4790
Evaluate side-chains
  67 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  138 LEU
Chi-restraints excluded: chain X residue  140 THR
Chi-restraints excluded: chain X residue  242 ILE
Chi-restraints excluded: chain X residue  382 ILE
Chi-restraints excluded: chain X residue  506 TYR
Chi-restraints excluded: chain X residue  515 CYS
Chi-restraints excluded: chain X residue  530 TYR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  140 THR
Chi-restraints excluded: chain H residue  149 CYS
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  208 ASN
Chi-restraints excluded: chain L residue  136 CYS
Chi-restraints excluded: chain L residue  196 CYS
Chi-restraints excluded: chain L residue  198 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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: 58.5591 > 50:
  distance: 9 - 159:  34.906
  distance: 38 - 178:  29.119
  distance: 41 - 175:  24.007
  distance: 51 - 163:  23.825
  distance: 53 - 160:  35.409
  distance: 109 - 111:  10.808
  distance: 111 - 112:  23.617
  distance: 112 - 113:  14.918
  distance: 112 - 115:   7.074
  distance: 113 - 114:  25.154
  distance: 113 - 118:  30.152
  distance: 115 - 116:  23.540
  distance: 115 - 117:  14.543
  distance: 118 - 119:  14.020
  distance: 119 - 120:  12.391
  distance: 119 - 122:   6.297
  distance: 120 - 121:   8.573
  distance: 120 - 127:   8.477
  distance: 122 - 123:  12.402
  distance: 123 - 124:  19.932
  distance: 124 - 125:  16.911
  distance: 124 - 126:   3.802
  distance: 127 - 128:  30.639
  distance: 128 - 129:  19.467
  distance: 128 - 131:  25.388
  distance: 129 - 130:  17.559
  distance: 129 - 134:  26.102
  distance: 131 - 132:  33.917
  distance: 131 - 133:  30.084
  distance: 134 - 135:  11.853
  distance: 135 - 136:  42.232
  distance: 135 - 138:  18.814
  distance: 136 - 137:  23.215
  distance: 136 - 146:  30.440
  distance: 138 - 139:  11.318
  distance: 139 - 140:   6.363
  distance: 139 - 141:  24.953
  distance: 140 - 142:  17.325
  distance: 141 - 143:  16.097
  distance: 142 - 144:  10.878
  distance: 143 - 144:  15.135
  distance: 144 - 145:  13.460
  distance: 146 - 147:  31.585
  distance: 147 - 148:  26.940
  distance: 147 - 150:  35.611
  distance: 148 - 149:  58.559
  distance: 148 - 154:  35.951
  distance: 150 - 151:  38.790
  distance: 150 - 152:  39.833
  distance: 151 - 153:  31.732
  distance: 154 - 155:  32.107
  distance: 154 - 253:  11.823
  distance: 155 - 156:   9.355
  distance: 155 - 158:  35.221
  distance: 156 - 157:   4.923
  distance: 156 - 160:   4.230
  distance: 157 - 250:  33.579
  distance: 158 - 159:  37.044
  distance: 160 - 161:  30.453
  distance: 161 - 162:  21.754
  distance: 161 - 164:  12.238
  distance: 162 - 163:  23.855
  distance: 162 - 168:   3.977
  distance: 164 - 165:  12.559
  distance: 165 - 166:  31.504
  distance: 165 - 167:  19.759
  distance: 168 - 169:  11.425
  distance: 168 - 238:  16.150
  distance: 169 - 170:   8.397
  distance: 169 - 172:   5.927
  distance: 170 - 171:  16.016
  distance: 170 - 175:  10.340
  distance: 171 - 235:  13.447
  distance: 172 - 173:  20.685
  distance: 172 - 174:  24.210
  distance: 175 - 176:   6.189
  distance: 176 - 177:   6.344
  distance: 176 - 179:  17.546
  distance: 177 - 178:  10.406
  distance: 177 - 183:  10.478
  distance: 179 - 180:  16.157
  distance: 180 - 181:   4.381
  distance: 180 - 182:  10.469
  distance: 183 - 184:   3.695
  distance: 183 - 223:  24.469
  distance: 184 - 185:  13.976
  distance: 184 - 187:  11.581
  distance: 185 - 186:  26.092
  distance: 185 - 193:  13.170
  distance: 186 - 220:  28.754
  distance: 187 - 188:  11.081
  distance: 188 - 189:  15.059
  distance: 188 - 190:  40.312
  distance: 189 - 191:   6.679
  distance: 190 - 192:   6.886
  distance: 191 - 192:  29.236