Starting phenix.real_space_refine
on Fri May 16 04:29:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ckz_30395/05_2025/7ckz_30395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ckz_30395/05_2025/7ckz_30395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ckz_30395/05_2025/7ckz_30395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ckz_30395/05_2025/7ckz_30395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ckz_30395/05_2025/7ckz_30395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ckz_30395/05_2025/7ckz_30395.cif"
  }
  resolution = 3.1
  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
-------------------------------------------------------------------------------
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=   0.005
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 7222 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
     S      53      5.16       5
     Cl      2      4.86       5
     C    5180      2.51       5
     N    1406      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8133
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1906
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2587
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2163
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 9, 'TRANS': 265}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 69
          Unusual residues: {'CLR': 1, 'G4C': 1, 'LDP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.00, per 1000 atoms: 0.61
  Number of scatterers: 8133
  At special positions: 0
  Unit cell: (96, 80, 125, 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)
     Cl      2     17.00
     S      53     16.00
     O    1492      8.00
     N    1406      7.00
     C    5180      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      43.1% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.864A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.155A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE A 285 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 281 through 285'
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 4.357A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.756A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.521A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 33
      removed outlier: 3.828A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.705A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.992A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 23 through 51
      removed outlier: 3.572A  pdb=" N   PHE R  51 " --> pdb=" O   ALA R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 76
      removed outlier: 3.624A  pdb=" N   PHE R  61 " --> pdb=" O   LYS R  57 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   PHE R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 95 through 127
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 161
      removed outlier: 4.621A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 191 through 203
      removed outlier: 3.849A  pdb=" N   SER R 197 " --> pdb=" O   THR R 193 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL R 200 " --> pdb=" O   ILE R 196 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE R 201 " --> pdb=" O   SER R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 237
      removed outlier: 4.324A  pdb=" N   ALA R 234 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 278
      removed outlier: 4.016A  pdb=" N   LYS R 269 " --> pdb=" O   LYS R 265 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU R 271 " --> pdb=" O   GLU R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 293
      Proline residue:  R 287  - end of helix
      removed outlier: 3.882A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 309 through 331
      removed outlier: 4.129A  pdb=" N   VAL R 315 " --> pdb=" O   ASN R 311 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASN R 323 " --> pdb=" O   PHE R 319 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 344
      removed outlier: 3.932A  pdb=" N   ALA R 340 " --> pdb=" O   ASP R 336 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR R 343 " --> pdb=" O   LYS R 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.505A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.899A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.714A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 4.039A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.644A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.584A  pdb=" N   PHE B 222 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.890A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.188A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
      removed outlier: 3.701A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU N  81 " --> pdb=" O   LEU N  20 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.498A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1167 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: 2.46

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1304
        1.31 -     1.44: 2324
        1.44 -     1.57: 4601
        1.57 -     1.70: 1
        1.70 -     1.82: 74
  Bond restraints: 8304
  Sorted by residual:
  bond pdb=" C05 G4C R 503 "
       pdb=" N04 G4C R 503 "
    ideal  model  delta    sigma   weight residual
    1.355  1.481 -0.126 2.00e-02 2.50e+03 3.96e+01
  bond pdb=" C16 G4C R 503 "
       pdb=" C18 G4C R 503 "
    ideal  model  delta    sigma   weight residual
    1.508  1.594 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" N   ARG N 105 "
       pdb=" CA  ARG N 105 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.18e-02 7.18e+03 7.80e+00
  bond pdb=" N   PHE B 234 "
       pdb=" CA  PHE B 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.25e-02 6.40e+03 6.34e+00
  bond pdb=" C08 G4C R 503 "
       pdb="CL9  G4C R 503 "
    ideal  model  delta    sigma   weight residual
    1.735  1.785 -0.050 2.00e-02 2.50e+03 6.18e+00
  ... (remaining 8299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11131
        1.88 -     3.75: 118
        3.75 -     5.63: 16
        5.63 -     7.50: 4
        7.50 -     9.38: 1
  Bond angle restraints: 11270
  Sorted by residual:
  angle pdb=" C03 G4C R 503 "
        pdb=" N04 G4C R 503 "
        pdb=" C05 G4C R 503 "
      ideal   model   delta    sigma   weight residual
     118.75  128.13   -9.38 3.00e+00 1.11e-01 9.77e+00
  angle pdb=" N   ARG N 105 "
        pdb=" CA  ARG N 105 "
        pdb=" C   ARG N 105 "
      ideal   model   delta    sigma   weight residual
     112.72  109.57    3.15 1.14e+00 7.69e-01 7.61e+00
  angle pdb=" N   VAL R 276 "
        pdb=" CA  VAL R 276 "
        pdb=" C   VAL R 276 "
      ideal   model   delta    sigma   weight residual
     111.81  109.50    2.31 8.60e-01 1.35e+00 7.24e+00
  angle pdb=" C06 G4C R 503 "
        pdb=" C05 G4C R 503 "
        pdb=" N04 G4C R 503 "
      ideal   model   delta    sigma   weight residual
     116.82  124.06   -7.24 3.00e+00 1.11e-01 5.82e+00
  angle pdb=" C03 G4C R 503 "
        pdb=" N04 G4C R 503 "
        pdb=" C16 G4C R 503 "
      ideal   model   delta    sigma   weight residual
     119.52  112.47    7.05 3.00e+00 1.11e-01 5.53e+00
  ... (remaining 11265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.78: 4656
       21.78 -    43.56: 271
       43.56 -    65.34: 38
       65.34 -    87.12: 10
       87.12 -   108.90: 6
  Dihedral angle restraints: 4981
    sinusoidal: 1959
      harmonic: 3022
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.36  -50.64     1      1.00e+01 1.00e-02 3.51e+01
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.75   34.25     1      1.00e+01 1.00e-02 1.66e+01
  dihedral pdb=" C02 G4C R 503 "
           pdb=" C03 G4C R 503 "
           pdb=" C30 G4C R 503 "
           pdb=" C19 G4C R 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.31  175.21 -108.90     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 4978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 796
       0.031 -    0.062: 351
       0.062 -    0.093: 94
       0.093 -    0.124: 37
       0.124 -    0.155: 4
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" C16 G4C R 503 "
            pdb=" C17 G4C R 503 "
            pdb=" C18 G4C R 503 "
            pdb=" N04 G4C R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.62    0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 1279 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 205 "    0.025 5.00e-02 4.00e+02   3.82e-02 2.33e+00
        pdb=" N   PRO R 206 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO R 206 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 206 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 332 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO G  49 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.24: 10
        2.24 -     2.90: 3347
        2.90 -     3.57: 12622
        3.57 -     4.23: 21827
        4.23 -     4.90: 35825
  Nonbonded interactions: 73631
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 119 "
            pdb=" O   GLY B 144 "
     model   vdw
     1.570 3.040
  nonbonded pdb=" OD1 ASN B 119 "
            pdb=" C   GLY B 144 "
     model   vdw
     1.910 3.270
  nonbonded pdb=" OG  SER R 202 "
            pdb=" O2  LDP R 502 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" O   ILE R 154 "
            pdb=" OH  TYR R 194 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" O   ALA R 101 "
            pdb=" OG  SER R 155 "
     model   vdw
     2.179 3.040
  ... (remaining 73626 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.200
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.126   8308  Z= 0.178
  Angle     :  0.519   9.377  11278  Z= 0.296
  Chirality :  0.039   0.155   1282
  Planarity :  0.003   0.038   1422
  Dihedral  : 14.328 108.900   3005
  Min Nonbonded Distance : 1.570

Molprobity Statistics.
  All-atom Clashscore : 22.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.14 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.23), residues: 1017
  helix: -1.83 (0.21), residues: 396
  sheet: -2.71 (0.31), residues: 200
  loop : -2.20 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.009   0.001   PHE R  20 
 TYR   0.009   0.001   TYR N 117 
 ARG   0.002   0.000   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22163 (  412)
  hydrogen bonds       : angle       8.40715 ( 1167)
  SS BOND              : bond        0.00779 (    4)
  SS BOND              : angle       1.07279 (    8)
  covalent geometry    : bond        0.00328 ( 8304)
  covalent geometry    : angle       0.51878 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 270
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.5446 (t80) cc_final: 0.4474 (t80)
REVERT: A  339 TYR cc_start: 0.8230 (m-80) cc_final: 0.7793 (m-80)
REVERT: A  343 ASP cc_start: 0.7415 (m-30) cc_final: 0.7078 (m-30)
REVERT: A  386 MET cc_start: 0.7538 (ttp) cc_final: 0.7265 (ttm)
REVERT: B  247 ASP cc_start: 0.8084 (p0) cc_final: 0.7806 (p0)
REVERT: N   94 TYR cc_start: 0.8186 (m-80) cc_final: 0.7947 (m-80)
REVERT: N   95 TYR cc_start: 0.8270 (m-80) cc_final: 0.7959 (m-80)
REVERT: R  156 PHE cc_start: 0.6519 (m-10) cc_final: 0.5909 (m-80)
REVERT: R  292 ASN cc_start: 0.8348 (t0) cc_final: 0.8064 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 274
  average time/residue: 0.2489
  time to fit residues: 86.9129
Evaluate side-chains
  210 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 207
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
A  41 HIS
A 267 GLN
A 271 ASN
A 278 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 259 GLN
B 266 HIS
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
N  13 GLN
N  31 ASN
N  39 GLN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.188128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.155542 restraints weight = 9293.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.06
r_work: 0.3667 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8308  Z= 0.158
  Angle     :  0.597  13.410  11278  Z= 0.307
  Chirality :  0.043   0.323   1282
  Planarity :  0.004   0.044   1422
  Dihedral  :  7.327  80.148   1215
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.51 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.25), residues: 1017
  helix: -0.48 (0.25), residues: 397
  sheet: -2.60 (0.33), residues: 191
  loop : -1.58 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.010   0.002   TYR B 264 
 ARG   0.007   0.001   ARG R 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04919 (  412)
  hydrogen bonds       : angle       5.93605 ( 1167)
  SS BOND              : bond        0.00194 (    4)
  SS BOND              : angle       0.95658 (    8)
  covalent geometry    : bond        0.00350 ( 8304)
  covalent geometry    : angle       0.59648 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 222
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8233 (tppt) cc_final: 0.7686 (mmtm)
REVERT: A  222 PHE cc_start: 0.6008 (t80) cc_final: 0.5046 (t80)
REVERT: A  255 MET cc_start: 0.0730 (mmm) cc_final: -0.1758 (mtp)
REVERT: A  271 ASN cc_start: 0.8083 (m110) cc_final: 0.7872 (m110)
REVERT: A  318 TYR cc_start: 0.7428 (t80) cc_final: 0.7070 (t80)
REVERT: A  339 TYR cc_start: 0.8590 (m-80) cc_final: 0.7895 (m-80)
REVERT: A  343 ASP cc_start: 0.8031 (m-30) cc_final: 0.7709 (m-30)
REVERT: B  124 TYR cc_start: 0.8887 (m-80) cc_final: 0.8572 (m-80)
REVERT: B  228 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7151 (m-30)
REVERT: B  323 ASP cc_start: 0.7776 (p0) cc_final: 0.7289 (p0)
REVERT: B  337 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8215 (mptt)
REVERT: R  142 ILE cc_start: 0.7533 (mt) cc_final: 0.7302 (mt)
REVERT: R  156 PHE cc_start: 0.6956 (m-10) cc_final: 0.6444 (m-80)
REVERT: R  319 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7596 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 232
  average time/residue: 0.2186
  time to fit residues: 66.6692
Evaluate side-chains
  212 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  295 LEU
Chi-restraints excluded: chain R residue  319 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0570
   chunk 46 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 5 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R  60 ASN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.184825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.150500 restraints weight = 9420.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.14
r_work: 0.3568 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8308  Z= 0.171
  Angle     :  0.571   9.606  11278  Z= 0.295
  Chirality :  0.042   0.204   1282
  Planarity :  0.004   0.046   1422
  Dihedral  :  5.493  53.361   1215
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.95 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.26), residues: 1017
  helix: -0.05 (0.26), residues: 404
  sheet: -2.42 (0.35), residues: 194
  loop : -1.38 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A  41 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.017   0.002   TYR B 264 
 ARG   0.012   0.001   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04311 (  412)
  hydrogen bonds       : angle       5.59448 ( 1167)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       1.10429 (    8)
  covalent geometry    : bond        0.00384 ( 8304)
  covalent geometry    : angle       0.57044 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 205
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8286 (tppt) cc_final: 0.7785 (mmtm)
REVERT: A  208 PHE cc_start: 0.3822 (m-80) cc_final: 0.3333 (t80)
REVERT: A  222 PHE cc_start: 0.5781 (t80) cc_final: 0.5283 (t80)
REVERT: A  294 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7567 (mm-40)
REVERT: A  318 TYR cc_start: 0.7596 (t80) cc_final: 0.7300 (t80)
REVERT: A  339 TYR cc_start: 0.8636 (m-80) cc_final: 0.8000 (m-80)
REVERT: A  343 ASP cc_start: 0.8141 (m-30) cc_final: 0.7844 (m-30)
REVERT: B  124 TYR cc_start: 0.8913 (m-80) cc_final: 0.8634 (m-80)
REVERT: B  228 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7270 (m-30)
REVERT: B  262 MET cc_start: 0.8635 (tpp) cc_final: 0.8346 (tpp)
REVERT: B  314 ARG cc_start: 0.8198 (ttt180) cc_final: 0.7973 (ptm160)
REVERT: B  337 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8262 (mttp)
REVERT: G   29 LYS cc_start: 0.8334 (mmtm) cc_final: 0.7953 (mmtm)
REVERT: N   95 TYR cc_start: 0.8878 (m-80) cc_final: 0.8330 (m-80)
REVERT: R   81 LYS cc_start: 0.8406 (tptt) cc_final: 0.7966 (tptt)
REVERT: R  142 ILE cc_start: 0.7577 (mt) cc_final: 0.7297 (mt)
  outliers start: 33
  outliers final: 23
  residues processed: 220
  average time/residue: 0.2176
  time to fit residues: 63.1075
Evaluate side-chains
  204 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    0.0670
   chunk 66 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
A 371 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.184118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149833 restraints weight = 9297.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.13
r_work: 0.3599 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8308  Z= 0.152
  Angle     :  0.549   6.727  11278  Z= 0.284
  Chirality :  0.041   0.135   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.680  54.130   1214
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.23 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.26), residues: 1017
  helix:  0.20 (0.26), residues: 403
  sheet: -2.40 (0.36), residues: 188
  loop : -1.27 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A  41 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.020   0.002   TYR B 264 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (  412)
  hydrogen bonds       : angle       5.41728 ( 1167)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       0.98364 (    8)
  covalent geometry    : bond        0.00343 ( 8304)
  covalent geometry    : angle       0.54862 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8269 (tppt) cc_final: 0.7799 (mmtm)
REVERT: A  208 PHE cc_start: 0.3921 (m-80) cc_final: 0.3407 (t80)
REVERT: A  222 PHE cc_start: 0.6057 (t80) cc_final: 0.5424 (t80)
REVERT: A  318 TYR cc_start: 0.7581 (t80) cc_final: 0.7318 (t80)
REVERT: A  332 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7931 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8351 (mtp-110)
REVERT: A  339 TYR cc_start: 0.8632 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  343 ASP cc_start: 0.8154 (m-30) cc_final: 0.7854 (m-30)
REVERT: B  262 MET cc_start: 0.8566 (tpp) cc_final: 0.8294 (tpp)
REVERT: B  323 ASP cc_start: 0.7971 (p0) cc_final: 0.7594 (p0)
REVERT: G   29 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7942 (mmtm)
REVERT: N   18 LEU cc_start: 0.7893 (tt) cc_final: 0.7685 (tp)
REVERT: N   95 TYR cc_start: 0.8912 (m-80) cc_final: 0.8258 (m-80)
REVERT: R  142 ILE cc_start: 0.7554 (mt) cc_final: 0.7243 (mt)
REVERT: R  154 ILE cc_start: 0.8518 (mm) cc_final: 0.8270 (mt)
  outliers start: 35
  outliers final: 23
  residues processed: 210
  average time/residue: 0.2086
  time to fit residues: 58.5141
Evaluate side-chains
  204 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 181
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  282 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 32 optimal weight:    0.3980
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 323 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.180851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.146312 restraints weight = 9217.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.11
r_work: 0.3554 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8308  Z= 0.171
  Angle     :  0.550   8.125  11278  Z= 0.287
  Chirality :  0.042   0.132   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.601  54.767   1213
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 20.81 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.26), residues: 1017
  helix:  0.30 (0.26), residues: 398
  sheet: -2.29 (0.35), residues: 197
  loop : -1.13 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.017   0.002   TYR B 264 
 ARG   0.006   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  412)
  hydrogen bonds       : angle       5.38463 ( 1167)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       1.03951 (    8)
  covalent geometry    : bond        0.00389 ( 8304)
  covalent geometry    : angle       0.54990 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 195
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8318 (tppt) cc_final: 0.7837 (mmtm)
REVERT: A  208 PHE cc_start: 0.3891 (OUTLIER) cc_final: 0.3631 (t80)
REVERT: A  222 PHE cc_start: 0.5984 (t80) cc_final: 0.5481 (t80)
REVERT: A  292 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8125 (m-40)
REVERT: A  318 TYR cc_start: 0.7651 (t80) cc_final: 0.7387 (t80)
REVERT: A  332 PRO cc_start: 0.8234 (Cg_exo) cc_final: 0.7895 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8388 (mtp-110)
REVERT: A  335 THR cc_start: 0.8738 (m) cc_final: 0.8473 (t)
REVERT: A  339 TYR cc_start: 0.8678 (m-80) cc_final: 0.8049 (m-80)
REVERT: A  343 ASP cc_start: 0.8152 (m-30) cc_final: 0.7879 (m-30)
REVERT: A  381 ASP cc_start: 0.7970 (m-30) cc_final: 0.7753 (m-30)
REVERT: B  124 TYR cc_start: 0.8933 (m-80) cc_final: 0.8707 (m-80)
REVERT: B  228 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7298 (m-30)
REVERT: B  262 MET cc_start: 0.8532 (tpp) cc_final: 0.8332 (mmm)
REVERT: B  289 TYR cc_start: 0.8888 (m-80) cc_final: 0.8665 (m-80)
REVERT: B  323 ASP cc_start: 0.8110 (p0) cc_final: 0.7730 (p0)
REVERT: N   87 LYS cc_start: 0.7589 (mttt) cc_final: 0.7343 (mmtm)
REVERT: R   81 LYS cc_start: 0.8559 (tptt) cc_final: 0.8098 (tptt)
REVERT: R  125 ILE cc_start: 0.8418 (mm) cc_final: 0.7697 (mt)
REVERT: R  142 ILE cc_start: 0.7637 (mt) cc_final: 0.7321 (mt)
REVERT: R  154 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8327 (mt)
  outliers start: 40
  outliers final: 28
  residues processed: 213
  average time/residue: 0.2071
  time to fit residues: 58.7940
Evaluate side-chains
  216 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 23 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 377 ASN
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.181390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.146810 restraints weight = 9308.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.13
r_work: 0.3558 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8308  Z= 0.155
  Angle     :  0.532   7.497  11278  Z= 0.279
  Chirality :  0.042   0.134   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.658  55.226   1213
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 21.51 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.27), residues: 1017
  helix:  0.34 (0.26), residues: 408
  sheet: -2.06 (0.37), residues: 181
  loop : -1.13 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A  41 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.013   0.002   TYR B 264 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  412)
  hydrogen bonds       : angle       5.32829 ( 1167)
  SS BOND              : bond        0.00221 (    4)
  SS BOND              : angle       1.00452 (    8)
  covalent geometry    : bond        0.00350 ( 8304)
  covalent geometry    : angle       0.53156 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8313 (tppt) cc_final: 0.7827 (mmtm)
REVERT: A  208 PHE cc_start: 0.3975 (OUTLIER) cc_final: 0.3703 (t80)
REVERT: A  222 PHE cc_start: 0.5934 (t80) cc_final: 0.5469 (t80)
REVERT: A  292 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8173 (m-40)
REVERT: A  318 TYR cc_start: 0.7652 (t80) cc_final: 0.7340 (t80)
REVERT: A  332 PRO cc_start: 0.8106 (Cg_exo) cc_final: 0.7762 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8423 (mtp-110)
REVERT: A  335 THR cc_start: 0.8749 (m) cc_final: 0.8538 (t)
REVERT: A  338 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8221 (ttmt)
REVERT: A  339 TYR cc_start: 0.8675 (m-80) cc_final: 0.8026 (m-80)
REVERT: A  343 ASP cc_start: 0.8154 (m-30) cc_final: 0.7875 (m-30)
REVERT: B  124 TYR cc_start: 0.8916 (m-80) cc_final: 0.8677 (m-80)
REVERT: B  197 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7484 (mmp80)
REVERT: B  228 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7256 (m-30)
REVERT: B  262 MET cc_start: 0.8490 (tpp) cc_final: 0.8252 (tpp)
REVERT: B  289 TYR cc_start: 0.8864 (m-80) cc_final: 0.8636 (m-80)
REVERT: B  323 ASP cc_start: 0.8066 (p0) cc_final: 0.7579 (p0)
REVERT: G   29 LYS cc_start: 0.8445 (tppt) cc_final: 0.7793 (mmtm)
REVERT: N   80 TYR cc_start: 0.8585 (m-80) cc_final: 0.8240 (m-80)
REVERT: N   87 LYS cc_start: 0.7554 (mttt) cc_final: 0.7311 (mmtm)
REVERT: N   95 TYR cc_start: 0.9044 (m-80) cc_final: 0.8501 (m-80)
REVERT: R   78 MET cc_start: 0.8310 (mtm) cc_final: 0.8085 (mtp)
REVERT: R  125 ILE cc_start: 0.8437 (mm) cc_final: 0.7720 (mt)
REVERT: R  142 ILE cc_start: 0.7683 (mt) cc_final: 0.7338 (mt)
REVERT: R  154 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8199 (mt)
REVERT: R  163 TRP cc_start: 0.6028 (m100) cc_final: 0.5710 (m100)
  outliers start: 38
  outliers final: 29
  residues processed: 211
  average time/residue: 0.2280
  time to fit residues: 64.5346
Evaluate side-chains
  215 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  271 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0570
   chunk 41 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 377 ASN
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.180917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.146542 restraints weight = 9357.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.11
r_work: 0.3530 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8308  Z= 0.156
  Angle     :  0.544   8.567  11278  Z= 0.283
  Chirality :  0.042   0.150   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.732  55.067   1213
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 21.63 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.27), residues: 1017
  helix:  0.45 (0.26), residues: 407
  sheet: -2.01 (0.37), residues: 181
  loop : -1.09 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  63 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.019   0.001   PHE A 363 
 TYR   0.013   0.002   TYR B 264 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  412)
  hydrogen bonds       : angle       5.26334 ( 1167)
  SS BOND              : bond        0.00222 (    4)
  SS BOND              : angle       1.01917 (    8)
  covalent geometry    : bond        0.00354 ( 8304)
  covalent geometry    : angle       0.54364 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 193
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8296 (tppt) cc_final: 0.7876 (mmtm)
REVERT: A   20 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7309 (ttm-80)
REVERT: A  222 PHE cc_start: 0.5871 (t80) cc_final: 0.5317 (t80)
REVERT: A  255 MET cc_start: 0.0813 (mmm) cc_final: -0.1178 (mtp)
REVERT: A  292 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8269 (m-40)
REVERT: A  318 TYR cc_start: 0.7680 (t80) cc_final: 0.7372 (t80)
REVERT: A  332 PRO cc_start: 0.8085 (Cg_exo) cc_final: 0.7754 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8734 (mtm180) cc_final: 0.8439 (mtp-110)
REVERT: A  335 THR cc_start: 0.8770 (m) cc_final: 0.8505 (t)
REVERT: A  338 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8331 (ttmt)
REVERT: A  339 TYR cc_start: 0.8702 (m-80) cc_final: 0.8039 (m-80)
REVERT: A  343 ASP cc_start: 0.8218 (m-30) cc_final: 0.7948 (m-30)
REVERT: A  374 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7454 (ttp-110)
REVERT: B  197 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7496 (mmp80)
REVERT: B  228 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7380 (m-30)
REVERT: B  262 MET cc_start: 0.8523 (tpp) cc_final: 0.8305 (tpp)
REVERT: G   29 LYS cc_start: 0.8441 (tppt) cc_final: 0.7766 (mmtm)
REVERT: N   80 TYR cc_start: 0.8562 (m-80) cc_final: 0.8213 (m-80)
REVERT: N   87 LYS cc_start: 0.7568 (mttt) cc_final: 0.7311 (mmtm)
REVERT: N   95 TYR cc_start: 0.9043 (m-80) cc_final: 0.8590 (m-80)
REVERT: R   81 LYS cc_start: 0.8560 (tptt) cc_final: 0.8219 (tptt)
REVERT: R  125 ILE cc_start: 0.8476 (mm) cc_final: 0.7772 (mt)
REVERT: R  142 ILE cc_start: 0.7744 (mt) cc_final: 0.7386 (mt)
REVERT: R  163 TRP cc_start: 0.6068 (m100) cc_final: 0.5807 (m100)
  outliers start: 40
  outliers final: 26
  residues processed: 212
  average time/residue: 0.2139
  time to fit residues: 60.6469
Evaluate side-chains
  213 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  271 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 10 optimal weight:    8.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
B  32 GLN
B 239 ASN
B 293 ASN
R  60 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.180571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146186 restraints weight = 9403.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.11
r_work: 0.3549 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8308  Z= 0.155
  Angle     :  0.552   8.630  11278  Z= 0.286
  Chirality :  0.042   0.141   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.756  55.292   1213
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 22.91 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.27), residues: 1017
  helix:  0.49 (0.26), residues: 407
  sheet: -1.96 (0.37), residues: 181
  loop : -1.08 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.025   0.002   PHE A 363 
 TYR   0.014   0.002   TYR B 124 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  412)
  hydrogen bonds       : angle       5.23125 ( 1167)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       0.98401 (    8)
  covalent geometry    : bond        0.00354 ( 8304)
  covalent geometry    : angle       0.55158 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8266 (tppt) cc_final: 0.7845 (mmtm)
REVERT: A   20 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7349 (ttm-80)
REVERT: A  208 PHE cc_start: 0.4591 (t80) cc_final: 0.3653 (t80)
REVERT: A  222 PHE cc_start: 0.5950 (t80) cc_final: 0.5463 (t80)
REVERT: A  265 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7865 (ttm170)
REVERT: A  292 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8214 (m-40)
REVERT: A  318 TYR cc_start: 0.7726 (t80) cc_final: 0.7422 (t80)
REVERT: A  332 PRO cc_start: 0.8103 (Cg_exo) cc_final: 0.7757 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8427 (mtp-110)
REVERT: A  335 THR cc_start: 0.8762 (m) cc_final: 0.8549 (t)
REVERT: A  338 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8366 (ttmt)
REVERT: A  339 TYR cc_start: 0.8706 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  343 ASP cc_start: 0.8195 (m-30) cc_final: 0.7948 (m-30)
REVERT: B  197 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7503 (mmp80)
REVERT: B  228 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7387 (m-30)
REVERT: B  262 MET cc_start: 0.8448 (tpp) cc_final: 0.8228 (tpp)
REVERT: B  289 TYR cc_start: 0.8878 (m-80) cc_final: 0.8677 (m-80)
REVERT: B  323 ASP cc_start: 0.8103 (p0) cc_final: 0.7700 (p0)
REVERT: B  335 PHE cc_start: 0.8135 (m-10) cc_final: 0.7876 (m-80)
REVERT: N   80 TYR cc_start: 0.8523 (m-80) cc_final: 0.8201 (m-80)
REVERT: N   95 TYR cc_start: 0.9045 (m-80) cc_final: 0.8606 (m-80)
REVERT: R   81 LYS cc_start: 0.8539 (tptt) cc_final: 0.8159 (tptt)
REVERT: R  142 ILE cc_start: 0.7815 (mt) cc_final: 0.7435 (mt)
REVERT: R  163 TRP cc_start: 0.6194 (m100) cc_final: 0.5955 (m100)
  outliers start: 35
  outliers final: 28
  residues processed: 203
  average time/residue: 0.2248
  time to fit residues: 60.5762
Evaluate side-chains
  212 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 377 ASN
R  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.180535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.146128 restraints weight = 9508.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.12
r_work: 0.3545 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8308  Z= 0.159
  Angle     :  0.567   9.778  11278  Z= 0.292
  Chirality :  0.042   0.157   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.785  55.848   1213
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 22.79 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.27), residues: 1017
  helix:  0.52 (0.26), residues: 407
  sheet: -1.92 (0.37), residues: 181
  loop : -1.10 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.027   0.002   PHE A 363 
 TYR   0.028   0.002   TYR A 360 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  412)
  hydrogen bonds       : angle       5.26154 ( 1167)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       0.97778 (    8)
  covalent geometry    : bond        0.00365 ( 8304)
  covalent geometry    : angle       0.56649 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8241 (tppt) cc_final: 0.7838 (mmtm)
REVERT: A   20 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7286 (ttm-80)
REVERT: A  208 PHE cc_start: 0.4733 (OUTLIER) cc_final: 0.3962 (t80)
REVERT: A  222 PHE cc_start: 0.5924 (t80) cc_final: 0.5484 (t80)
REVERT: A  265 ARG cc_start: 0.8263 (ttt90) cc_final: 0.7882 (ttm170)
REVERT: A  292 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (m-40)
REVERT: A  318 TYR cc_start: 0.7735 (t80) cc_final: 0.7461 (t80)
REVERT: A  332 PRO cc_start: 0.8100 (Cg_exo) cc_final: 0.7751 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8460 (mtp-110)
REVERT: A  335 THR cc_start: 0.8762 (m) cc_final: 0.8550 (t)
REVERT: A  338 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8327 (ttmt)
REVERT: A  339 TYR cc_start: 0.8699 (m-80) cc_final: 0.8088 (m-80)
REVERT: A  343 ASP cc_start: 0.8218 (m-30) cc_final: 0.7991 (m-30)
REVERT: B  197 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7533 (mmp80)
REVERT: B  228 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7375 (m-30)
REVERT: B  262 MET cc_start: 0.8361 (tpp) cc_final: 0.8037 (tpp)
REVERT: B  323 ASP cc_start: 0.8145 (p0) cc_final: 0.7705 (p0)
REVERT: G   22 GLU cc_start: 0.7372 (tt0) cc_final: 0.6897 (mt-10)
REVERT: N   80 TYR cc_start: 0.8502 (m-80) cc_final: 0.8196 (m-80)
REVERT: N   95 TYR cc_start: 0.9070 (m-80) cc_final: 0.8581 (m-80)
REVERT: R   81 LYS cc_start: 0.8545 (tptt) cc_final: 0.8133 (tptt)
REVERT: R  142 ILE cc_start: 0.7801 (mt) cc_final: 0.7424 (mt)
REVERT: R  163 TRP cc_start: 0.6174 (m100) cc_final: 0.5916 (m100)
  outliers start: 35
  outliers final: 29
  residues processed: 209
  average time/residue: 0.2099
  time to fit residues: 58.8569
Evaluate side-chains
  217 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  271 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.178944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144449 restraints weight = 9319.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.10
r_work: 0.3527 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8308  Z= 0.190
  Angle     :  0.595   9.340  11278  Z= 0.306
  Chirality :  0.043   0.156   1282
  Planarity :  0.004   0.047   1422
  Dihedral  :  4.886  55.923   1213
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.14 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.27), residues: 1017
  helix:  0.55 (0.26), residues: 405
  sheet: -1.94 (0.37), residues: 181
  loop : -1.18 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.033   0.002   PHE A 363 
 TYR   0.029   0.002   TYR A 360 
 ARG   0.006   0.001   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  412)
  hydrogen bonds       : angle       5.29138 ( 1167)
  SS BOND              : bond        0.00279 (    4)
  SS BOND              : angle       1.11722 (    8)
  covalent geometry    : bond        0.00437 ( 8304)
  covalent geometry    : angle       0.59397 (11270)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 193
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8248 (tppt) cc_final: 0.7857 (mmtm)
REVERT: A   20 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7303 (ttm-80)
REVERT: A   31 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7788 (mm110)
REVERT: A  208 PHE cc_start: 0.4901 (t80) cc_final: 0.4451 (t80)
REVERT: A  222 PHE cc_start: 0.5979 (t80) cc_final: 0.5629 (t80)
REVERT: A  265 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7837 (ttm170)
REVERT: A  292 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (m-40)
REVERT: A  294 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7955 (mm-40)
REVERT: A  318 TYR cc_start: 0.7838 (t80) cc_final: 0.7563 (t80)
REVERT: A  332 PRO cc_start: 0.8105 (Cg_exo) cc_final: 0.7874 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8453 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8259 (ttmt)
REVERT: A  339 TYR cc_start: 0.8703 (m-80) cc_final: 0.8091 (m-80)
REVERT: A  343 ASP cc_start: 0.8225 (m-30) cc_final: 0.8003 (m-30)
REVERT: B  228 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7459 (m-30)
REVERT: B  262 MET cc_start: 0.8331 (tpp) cc_final: 0.8055 (tpp)
REVERT: B  323 ASP cc_start: 0.8126 (p0) cc_final: 0.7761 (p0)
REVERT: B  329 THR cc_start: 0.9024 (m) cc_final: 0.8817 (p)
REVERT: G   22 GLU cc_start: 0.7416 (tt0) cc_final: 0.6937 (mt-10)
REVERT: N   80 TYR cc_start: 0.8502 (m-80) cc_final: 0.8173 (m-80)
REVERT: N   95 TYR cc_start: 0.9077 (m-80) cc_final: 0.8554 (m-80)
REVERT: R   81 LYS cc_start: 0.8494 (tptt) cc_final: 0.8048 (tptt)
REVERT: R  142 ILE cc_start: 0.7831 (mt) cc_final: 0.7459 (mt)
REVERT: R  163 TRP cc_start: 0.6146 (m100) cc_final: 0.5894 (m100)
  outliers start: 35
  outliers final: 30
  residues processed: 210
  average time/residue: 0.1944
  time to fit residues: 55.2153
Evaluate side-chains
  221 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  271 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 54.1748 > 50:
  distance: 31 - 57:   4.229
  distance: 42 - 63:   8.043
  distance: 46 - 51:   7.547
  distance: 51 - 52:  11.419
  distance: 52 - 53:   9.719
  distance: 52 - 55:  17.720
  distance: 53 - 54:  16.184
  distance: 53 - 57:  12.928
  distance: 55 - 56:  27.536
  distance: 57 - 58:   5.848
  distance: 58 - 59:   5.032
  distance: 58 - 61:   6.977
  distance: 59 - 60:  14.175
  distance: 59 - 63:   8.532
  distance: 60 - 84:  31.979
  distance: 61 - 62:   8.956
  distance: 63 - 64:   3.723
  distance: 64 - 65:   7.161
  distance: 64 - 67:  16.738
  distance: 65 - 66:  11.137
  distance: 65 - 69:  19.339
  distance: 66 - 90:  33.881
  distance: 67 - 68:  17.892
  distance: 69 - 70:  14.194
  distance: 70 - 71:   7.000
  distance: 70 - 73:   8.881
  distance: 71 - 72:  27.800
  distance: 71 - 76:  28.195
  distance: 73 - 74:   6.645
  distance: 73 - 75:  36.665
  distance: 76 - 77:   7.322
  distance: 77 - 78:  27.315
  distance: 77 - 80:   8.168
  distance: 78 - 79:  13.539
  distance: 78 - 84:  17.787
  distance: 80 - 81:  21.919
  distance: 80 - 82:  22.428
  distance: 81 - 83:  47.683
  distance: 84 - 85:  18.658
  distance: 85 - 86:   9.712
  distance: 85 - 88:   9.520
  distance: 86 - 87:   5.234
  distance: 86 - 90:   7.816
  distance: 88 - 89:  19.753
  distance: 90 - 91:   7.980
  distance: 91 - 92:   7.310
  distance: 91 - 94:   9.596
  distance: 92 - 93:  11.222
  distance: 92 - 101:   7.450
  distance: 93 - 128:  10.050
  distance: 94 - 95:   5.347
  distance: 95 - 96:  11.656
  distance: 95 - 97:  14.713
  distance: 96 - 98:  12.812
  distance: 97 - 99:  15.740
  distance: 98 - 100:  13.211
  distance: 99 - 100:  17.354
  distance: 101 - 102:  11.568
  distance: 102 - 103:   9.938
  distance: 102 - 105:  11.031
  distance: 103 - 104:  24.039
  distance: 103 - 113:  15.536
  distance: 104 - 135:  30.583
  distance: 105 - 106:  14.299
  distance: 106 - 107:  11.045
  distance: 106 - 108:   3.064
  distance: 107 - 109:   8.632
  distance: 108 - 110:   5.032
  distance: 109 - 111:  11.949
  distance: 110 - 111:   3.325
  distance: 111 - 112:  12.885
  distance: 113 - 114:  20.349
  distance: 114 - 115:  18.526
  distance: 114 - 117:  13.228
  distance: 115 - 116:  17.657
  distance: 115 - 121:   8.646
  distance: 116 - 139:  13.445
  distance: 117 - 118:   6.256
  distance: 117 - 119:  21.690
  distance: 118 - 120:  27.907
  distance: 121 - 122:   6.664
  distance: 121 - 127:  19.933
  distance: 122 - 123:  19.800
  distance: 122 - 125:   9.196
  distance: 123 - 124:   8.651
  distance: 123 - 128:   7.303
  distance: 124 - 147:  10.438
  distance: 125 - 126:   9.372
  distance: 126 - 127:  11.810