Starting phenix.real_space_refine
on Tue Jun 10 01:17:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7arm_11887/06_2025/7arm_11887.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7arm_11887/06_2025/7arm_11887.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7arm_11887/06_2025/7arm_11887.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7arm_11887/06_2025/7arm_11887.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7arm_11887/06_2025/7arm_11887.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7arm_11887/06_2025/7arm_11887.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 56 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: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    6974      2.51       5
     N    1931      2.21       5
     O    2013      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10971
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 2969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 2969
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 20, 'TRANS': 371}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 3159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3159
          Classifications: {'peptide': 409}
          Link IDs: {'PTRANS': 14, 'TRANS': 394}
    Chain: "F"
      Number of atoms: 1614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1614
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 8, 'TRANS': 212}
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 37
    Chain: "D"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1663
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 8, 'TRANS': 215}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "V"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 73
          Classifications: {'peptide': 10}
          Link IDs: {'TRANS': 9}
    Chain: "A"
      Number of atoms: 1437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1437
          Classifications: {'peptide': 182}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 174}
    Chain: "V"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'PLM': 1, 'Z41': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 6.65, per 1000 atoms: 0.61
  Number of scatterers: 10971
  At special positions: 0
  Unit cell: (104.442, 161.226, 134.862, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    2013      8.00
     N    1931      7.00
     C    6974      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2638

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 14 sheets defined
      37.7% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 10
      removed outlier: 4.033A  pdb=" N   GLY C  10 " --> pdb=" O   ALA C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 26
      removed outlier: 3.593A  pdb=" N   ARG C  24 " --> pdb=" O   ASP C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 55
      removed outlier: 3.574A  pdb=" N   ILE C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY C  37 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   MET C  39 " --> pdb=" O   THR C  35 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU C  45 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL C  47 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 137
      removed outlier: 3.864A  pdb=" N   LEU C 137 " --> pdb=" O   GLN C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 155
      removed outlier: 3.584A  pdb=" N   GLN C 153 " --> pdb=" O   GLN C 149 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C 154 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 198
      removed outlier: 3.766A  pdb=" N   GLY C 198 " --> pdb=" O   GLU C 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 195 through 198'
    Processing helix  chain 'C' and resid 248 through 252
      removed outlier: 4.048A  pdb=" N   ASP C 251 " --> pdb=" O   ASP C 248 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG C 252 " --> pdb=" O   TRP C 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 248 through 252'
    Processing helix  chain 'C' and resid 253 through 271
      removed outlier: 3.700A  pdb=" N   PHE C 257 " --> pdb=" O   LYS C 253 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA C 259 " --> pdb=" O   GLU C 255 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C 260 " --> pdb=" O   LEU C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 293
      removed outlier: 3.722A  pdb=" N   ILE C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE C 283 " --> pdb=" O   ALA C 279 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU C 288 " --> pdb=" O   THR C 284 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET C 289 " --> pdb=" O   SER C 285 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL C 290 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   MET C 291 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 302
      removed outlier: 3.720A  pdb=" N   ALA C 298 " --> pdb=" O   GLN C 294 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE C 299 " --> pdb=" O   GLY C 295 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN C 301 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR C 302 " --> pdb=" O   ALA C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 337
      removed outlier: 4.013A  pdb=" N   MET C 312 " --> pdb=" O   ARG C 308 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL C 313 " --> pdb=" O   GLN C 309 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   PHE C 314 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLN C 317 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY C 318 " --> pdb=" O   PHE C 314 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ALA C 321 " --> pdb=" O   GLN C 317 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   GLY C 322 " --> pdb=" O   GLY C 318 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU C 335 " --> pdb=" O   ALA C 331 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA C 337 " --> pdb=" O   GLY C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 348
      removed outlier: 4.071A  pdb=" N   ILE C 347 " --> pdb=" O   MET C 344 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY C 348 " --> pdb=" O   PRO C 345 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 344 through 348'
    Processing helix  chain 'C' and resid 361 through 379
      removed outlier: 3.569A  pdb=" N   VAL C 365 " --> pdb=" O   GLU C 361 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE C 366 " --> pdb=" O   PRO C 362 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL C 367 " --> pdb=" O   LEU C 363 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA C 376 " --> pdb=" O   ALA C 372 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LEU C 377 " --> pdb=" O   MET C 373 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 389
      removed outlier: 3.722A  pdb=" N   ARG C 386 " --> pdb=" O   TYR C 382 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA C 387 " --> pdb=" O   PRO C 383 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 6 through 11
      removed outlier: 4.060A  pdb=" N   LEU E  11 " --> pdb=" O   LEU E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 59
      removed outlier: 3.919A  pdb=" N   ILE E  26 " --> pdb=" O   MET E  22 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL E  28 " --> pdb=" O   SER E  24 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR E  31 " --> pdb=" O   SER E  27 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE E  34 " --> pdb=" O   SER E  30 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   GLY E  37 " --> pdb=" O   GLY E  33 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL E  38 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL E  43 " --> pdb=" O   ALA E  39 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA E  47 " --> pdb=" O   VAL E  43 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASN E  56 " --> pdb=" O   GLU E  52 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ASN E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 85
      removed outlier: 4.014A  pdb=" N   ASP E  83 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL E  85 " --> pdb=" O   ALA E  81 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 126
      removed outlier: 3.599A  pdb=" N   ARG E 125 " --> pdb=" O   GLN E 122 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU E 126 " --> pdb=" O   GLU E 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 122 through 126'
    Processing helix  chain 'E' and resid 129 through 133
      removed outlier: 3.713A  pdb=" N   PHE E 132 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL E 133 " --> pdb=" O   PRO E 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 129 through 133'
    Processing helix  chain 'E' and resid 152 through 159
      removed outlier: 3.647A  pdb=" N   ASP E 156 " --> pdb=" O   LYS E 152 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA E 157 " --> pdb=" O   GLY E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 212
      removed outlier: 3.689A  pdb=" N   GLN E 212 " --> pdb=" O   LEU E 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 208 through 212'
    Processing helix  chain 'E' and resid 235 through 244
      removed outlier: 3.759A  pdb=" N   ARG E 239 " --> pdb=" O   ASN E 235 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASP E 240 " --> pdb=" O   LYS E 236 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA E 241 " --> pdb=" O   LEU E 237 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU E 243 " --> pdb=" O   ARG E 239 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL E 244 " --> pdb=" O   ASP E 240 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 258 through 263
      removed outlier: 3.702A  pdb=" N   TYR E 262 " --> pdb=" O   TYR E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 267 through 284
      removed outlier: 4.294A  pdb=" N   TYR E 273 " --> pdb=" O   ARG E 269 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU E 274 " --> pdb=" O   ALA E 270 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU E 278 " --> pdb=" O   LEU E 274 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL E 279 " --> pdb=" O   ALA E 275 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 298
      removed outlier: 3.731A  pdb=" N   MET E 293 " --> pdb=" O   SER E 289 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA E 294 " --> pdb=" O   THR E 290 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS E 296 " --> pdb=" O   VAL E 292 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS E 298 " --> pdb=" O   ALA E 294 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 308
      removed outlier: 3.505A  pdb=" N   ILE E 302 " --> pdb=" O   LYS E 298 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA E 303 " --> pdb=" O   SER E 299 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU E 305 " --> pdb=" O   ASP E 301 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 311 through 336
      removed outlier: 3.622A  pdb=" N   ILE E 315 " --> pdb=" O   LYS E 311 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE E 319 " --> pdb=" O   ILE E 315 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TRP E 321 " --> pdb=" O   ALA E 317 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA E 326 " --> pdb=" O   TYR E 322 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLY E 330 " --> pdb=" O   ALA E 326 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   CYS E 333 " --> pdb=" O   PHE E 329 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 345 through 353
      removed outlier: 3.820A  pdb=" N   GLU E 350 " --> pdb=" O   THR E 346 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TRP E 351 " --> pdb=" O   PRO E 347 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE E 352 " --> pdb=" O   ILE E 348 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 376 through 402
      removed outlier: 3.904A  pdb=" N   VAL E 380 " --> pdb=" O   HIS E 376 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   PHE E 381 " --> pdb=" O   TRP E 377 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL E 383 " --> pdb=" O   ASP E 379 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER E 391 " --> pdb=" O   ALA E 387 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   TYR E 397 " --> pdb=" O   LEU E 393 " (cutoff:3.500A)
      Proline residue:  E 398  - end of helix
      removed outlier: 3.501A  pdb=" N   ARG E 401 " --> pdb=" O   TYR E 397 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 55
      removed outlier: 3.790A  pdb=" N   HIS F  53 " --> pdb=" O   SER F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 108
      removed outlier: 4.047A  pdb=" N   VAL F 108 " --> pdb=" O   ALA F 104 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 115
      removed outlier: 3.651A  pdb=" N   ILE F 114 " --> pdb=" O   MET F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 118 through 129
      removed outlier: 3.722A  pdb=" N   ASN F 123 " --> pdb=" O   PRO F 119 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER F 124 " --> pdb=" O   ALA F 120 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU F 127 " --> pdb=" O   ASN F 123 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU F 128 " --> pdb=" O   SER F 124 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 134
    Processing helix  chain 'F' and resid 147 through 160
      removed outlier: 3.565A  pdb=" N   GLN F 152 " --> pdb=" O   GLY F 148 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG F 153 " --> pdb=" O   GLY F 149 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL F 154 " --> pdb=" O   GLU F 150 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA F 155 " --> pdb=" O   ARG F 151 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE F 156 " --> pdb=" O   GLN F 152 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA F 157 " --> pdb=" O   ARG F 153 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA F 159 " --> pdb=" O   ALA F 155 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU F 160 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 191
      removed outlier: 4.664A  pdb=" N   ASP F 182 " --> pdb=" O   ALA F 178 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   SER F 183 " --> pdb=" O   ARG F 179 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE F 184 " --> pdb=" O   ASN F 180 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE F 185 " --> pdb=" O   ALA F 181 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU F 191 " --> pdb=" O   LEU F 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 55
      removed outlier: 3.825A  pdb=" N   LEU D  54 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU D  55 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 50 through 55'
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.983A  pdb=" N   VAL D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 115
      removed outlier: 3.517A  pdb=" N   GLY D 115 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 122
      removed outlier: 4.095A  pdb=" N   ILE D 122 " --> pdb=" O   PRO D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 124 through 132
      removed outlier: 3.607A  pdb=" N   LEU D 130 " --> pdb=" O   ALA D 126 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA D 132 " --> pdb=" O   GLU D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 146
      removed outlier: 3.615A  pdb=" N   GLU D 145 " --> pdb=" O   ARG D 142 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU D 146 " --> pdb=" O   PRO D 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 142 through 146'
    Processing helix  chain 'D' and resid 147 through 158
      removed outlier: 3.611A  pdb=" N   GLN D 152 " --> pdb=" O   GLY D 148 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG D 153 " --> pdb=" O   GLY D 149 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL D 154 " --> pdb=" O   GLU D 150 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA D 155 " --> pdb=" O   ARG D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 190
      removed outlier: 3.674A  pdb=" N   ALA D 181 " --> pdb=" O   ASP D 177 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASP D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER D 183 " --> pdb=" O   ARG D 179 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU D 187 " --> pdb=" O   SER D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 193
      No H-bonds generated for 'chain 'D' and resid 191 through 193'
    Processing helix  chain 'D' and resid 205 through 209
      removed outlier: 3.926A  pdb=" N   LEU D 208 " --> pdb=" O   ASP D 205 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ALA D 209 " --> pdb=" O   LEU D 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 205 through 209'
    Processing helix  chain 'A' and resid 1 through 5
      removed outlier: 4.311A  pdb=" N   SER A   4 " --> pdb=" O   ASP A   1 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP A   5 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1 through 5'
    Processing helix  chain 'A' and resid 88 through 96
      removed outlier: 4.101A  pdb=" N   LEU A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE A  93 " --> pdb=" O   PRO A  89 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA A  94 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASN A  96 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
    Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69
    Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96
      removed outlier: 4.705A  pdb=" N   ARG C  92 " --> pdb=" O   TRP C 225 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TRP C 225 " --> pdb=" O   ARG C  92 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY C 221 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 98 through 104
      removed outlier: 3.670A  pdb=" N   GLY C  99 " --> pdb=" O   MET C 114 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   MET C 201 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL C 113 " --> pdb=" O   MET C 201 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   VAL C 203 " --> pdb=" O   VAL C 113 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   LEU C 115 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ASN C 204 " --> pdb=" O   ASN C 143 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ASN C 143 " --> pdb=" O   ASN C 204 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER C 180 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET C 165 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 67 through 69
      removed outlier: 3.694A  pdb=" N   GLU E  67 " --> pdb=" O   LYS E 252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 96
      removed outlier: 4.087A  pdb=" N   ALA E  93 " --> pdb=" O   LYS E 227 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 98 through 104
      removed outlier: 3.624A  pdb=" N   GLY E 102 " --> pdb=" O   ILE E 113 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG E 111 " --> pdb=" O   VAL E 104 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   ALA E 204 " --> pdb=" O   ALA E 112 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   GLN E 114 " --> pdb=" O   ALA E 204 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   ILE E 206 " --> pdb=" O   GLN E 114 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LYS E 116 " --> pdb=" O   ILE E 206 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   MET E 205 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE E 149 " --> pdb=" O   MET E 205 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   GLN E 147 " --> pdb=" O   PRO E 207 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE E 150 " --> pdb=" O   ALA E 190 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ILE E 192 " --> pdb=" O   ILE E 150 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 14 through 16
    Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 41
      removed outlier: 6.309A  pdb=" N   MET F  38 " --> pdb=" O   VAL F 201 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   THR F 203 " --> pdb=" O   MET F  38 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ILE F  40 " --> pdb=" O   THR F 203 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ILE F  92 " --> pdb=" O   ASP F 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13
    Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 91
      removed outlier: 5.707A  pdb=" N   GLY D  90 " --> pdb=" O   LEU D 168 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL D 167 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 47 through 50
      removed outlier: 3.932A  pdb=" N   ALA A  18 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 31 through 35
      removed outlier: 5.238A  pdb=" N   GLN A  33 " --> pdb=" O   VAL A  24 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL A  24 " --> pdb=" O   GLN A  33 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLN A 148 " --> pdb=" O   GLU A 144 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A 150 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA A 142 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   GLN A 126 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 66 through 70
    Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 131
      removed outlier: 6.274A  pdb=" N   ASN A 130 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    786 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: 2.73

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3604
        1.34 -     1.46: 1430
        1.46 -     1.57: 6026
        1.57 -     1.69: 0
        1.69 -     1.81: 99
  Bond restraints: 11159
  Sorted by residual:
  bond pdb=" C16 Z41 V 101 "
       pdb=" O2  Z41 V 101 "
    ideal  model  delta    sigma   weight residual
    1.332  1.454 -0.122 2.00e-02 2.50e+03 3.72e+01
  bond pdb=" C19 Z41 V 101 "
       pdb=" O3  Z41 V 101 "
    ideal  model  delta    sigma   weight residual
    1.333  1.455 -0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" C   ARG A  43 "
       pdb=" N   PRO A  44 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.054 2.34e-02 1.83e+03 5.24e+00
  bond pdb=" C   GLN A  53 "
       pdb=" N   PRO A  54 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.95e+00
  bond pdb=" CA  THR F  62 "
       pdb=" CB  THR F  62 "
    ideal  model  delta    sigma   weight residual
    1.530  1.552 -0.022 1.69e-02 3.50e+03 1.70e+00
  ... (remaining 11154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 14836
        2.39 -     4.78: 216
        4.78 -     7.16: 44
        7.16 -     9.55: 6
        9.55 -    11.94: 2
  Bond angle restraints: 15104
  Sorted by residual:
  angle pdb=" N   ILE E 356 "
        pdb=" CA  ILE E 356 "
        pdb=" C   ILE E 356 "
      ideal   model   delta    sigma   weight residual
     113.47  108.97    4.50 1.01e+00 9.80e-01 1.98e+01
  angle pdb=" C   PRO F  61 "
        pdb=" N   THR F  62 "
        pdb=" CA  THR F  62 "
      ideal   model   delta    sigma   weight residual
     121.54  130.03   -8.49 1.91e+00 2.74e-01 1.98e+01
  angle pdb=" C   GLN A 103 "
        pdb=" N   TYR A 104 "
        pdb=" CA  TYR A 104 "
      ideal   model   delta    sigma   weight residual
     122.82  128.64   -5.82 1.42e+00 4.96e-01 1.68e+01
  angle pdb=" C   GLY F 115 "
        pdb=" N   LYS F 116 "
        pdb=" CA  LYS F 116 "
      ideal   model   delta    sigma   weight residual
     122.82  127.92   -5.10 1.42e+00 4.96e-01 1.29e+01
  angle pdb=" CA  LEU D 160 "
        pdb=" CB  LEU D 160 "
        pdb=" CG  LEU D 160 "
      ideal   model   delta    sigma   weight residual
     116.30  128.24  -11.94 3.50e+00 8.16e-02 1.16e+01
  ... (remaining 15099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 6149
       17.48 -    34.95: 479
       34.95 -    52.43: 92
       52.43 -    69.91: 19
       69.91 -    87.38: 8
  Dihedral angle restraints: 6747
    sinusoidal: 2653
      harmonic: 4094
  Sorted by residual:
  dihedral pdb=" CA  PRO E  74 "
           pdb=" C   PRO E  74 "
           pdb=" N   TRP E  75 "
           pdb=" CA  TRP E  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.10   19.90     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  ARG A  43 "
           pdb=" C   ARG A  43 "
           pdb=" N   PRO A  44 "
           pdb=" CA  PRO A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.66  -19.34     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  MET C  63 "
           pdb=" C   MET C  63 "
           pdb=" N   PRO C  64 "
           pdb=" CA  PRO C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 6744 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1207
       0.042 -    0.083: 378
       0.083 -    0.125: 130
       0.125 -    0.166: 23
       0.166 -    0.208: 4
  Chirality restraints: 1742
  Sorted by residual:
  chirality pdb=" CB  ILE E 149 "
            pdb=" CA  ILE E 149 "
            pdb=" CG1 ILE E 149 "
            pdb=" CG2 ILE E 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE C 178 "
            pdb=" CA  ILE C 178 "
            pdb=" CG1 ILE C 178 "
            pdb=" CG2 ILE C 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CB  ILE D   4 "
            pdb=" CA  ILE D   4 "
            pdb=" CG1 ILE D   4 "
            pdb=" CG2 ILE D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.41e-01
  ... (remaining 1739 not shown)

  Planarity restraints: 1950
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 178 "    0.041 5.00e-02 4.00e+02   6.29e-02 6.33e+00
        pdb=" N   PRO C 179 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO C 179 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 179 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D 110 "    0.037 5.00e-02 4.00e+02   5.45e-02 4.76e+00
        pdb=" N   PRO D 111 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D 111 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 111 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 346 "    0.036 5.00e-02 4.00e+02   5.35e-02 4.57e+00
        pdb=" N   PRO E 347 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO E 347 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 347 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1947 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3502
        2.84 -     3.36: 8703
        3.36 -     3.87: 16984
        3.87 -     4.39: 19180
        4.39 -     4.90: 32738
  Nonbonded interactions: 81107
  Sorted by model distance:
  nonbonded pdb=" O   PRO E  74 "
            pdb=" OG  SER E 220 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   LEU F   6 "
            pdb=" OG  SER F  31 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   SER E 342 "
            pdb=" OG  SER E 373 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   ALA E  61 "
            pdb=" OG  SER E 127 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   CYS D   8 "
            pdb=" OG  SER D  29 "
     model   vdw
     2.371 3.040
  ... (remaining 81102 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'D' and (resid 3 through 12 or (resid 13 through 14 and (name N or name C \ 
A or name C or name O or name CB )) or resid 15 or (resid 16 through 17 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 18 through 19 or (resi \ 
d 20 and (name N or name CA or name C or name O or name CB )) or resid 21 throug \ 
h 27 or (resid 28 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 29 through 35 or (resid 36 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 37 through 47 or (resid 48 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 49 through 54 or (resid 55 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 56 through 59 or (resid 60 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 61 through 64 or (resid  \ 
65 and (name N or name CA or name C or name O or name CB )) or resid 66 through  \ 
75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 77 through 132 or (resid 133 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 134 or (resid 135 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 136 through 170 or (resid 171 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 172 through 175 or (resid 176 through 178 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 179 through 211 \ 
 or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 
 213 through 215 or (resid 216 through 217 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 218 through 222 or (resid 223 and (name N or name C \ 
A or name C or name O or name CB ))))
  selection = (chain 'F' and (resid 3 through 164 or (resid 165 through 166 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 167 through 172 or (resid 173 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 174 through 181  \ 
or (resid 182 and (name N or name CA or name C or name O or name CB )) or resid  \ 
183 through 186 or (resid 187 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 188 through 200 or (resid 201 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 202 through 214 or (resid 215 through 217 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 218 through 221 or ( \ 
resid 222 through 223 and (name N or name CA or name C or name O or name CB )))) \ 

}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     26.580
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
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   0.122  11161  Z= 0.178
  Angle     :  0.698  11.942  15104  Z= 0.355
  Chirality :  0.047   0.208   1742
  Planarity :  0.005   0.063   1950
  Dihedral  : 13.162  87.384   4109
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  6.69 %
    Favored  : 93.14 %
  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: -5.79 (0.14), residues: 1424
  helix: -5.09 (0.05), residues: 449
  sheet: -2.44 (0.36), residues: 155
  loop : -3.50 (0.15), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 101 
 HIS   0.003   0.000   HIS A  50 
 PHE   0.030   0.001   PHE D  30 
 TYR   0.010   0.001   TYR A 104 
 ARG   0.002   0.000   ARG F 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.34501 (  275)
  hydrogen bonds       : angle      10.63445 (  786)
  covalent geometry    : bond        0.00320 (11159)
  covalent geometry    : angle       0.69827 (15104)
  Misc. bond           : bond        0.05176 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 371
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   48 MET cc_start: 0.7930 (mtp) cc_final: 0.7641 (mtp)
REVERT: C  117 ILE cc_start: 0.8934 (pt) cc_final: 0.8727 (pt)
REVERT: E   12 ARG cc_start: 0.4395 (mmp80) cc_final: 0.3681 (mmt180)
REVERT: E  136 ASP cc_start: 0.7304 (t0) cc_final: 0.7097 (t0)
REVERT: E  382 TYR cc_start: 0.7600 (m-10) cc_final: 0.7394 (m-10)
REVERT: F  106 GLU cc_start: 0.6841 (pt0) cc_final: 0.6434 (mt-10)
REVERT: F  129 MET cc_start: 0.7170 (mmm) cc_final: 0.6811 (tpp)
REVERT: F  191 LEU cc_start: 0.8227 (mp) cc_final: 0.7716 (mp)
REVERT: D   86 ASN cc_start: 0.6854 (p0) cc_final: 0.6267 (t0)
REVERT: V   10 LEU cc_start: 0.4279 (mt) cc_final: 0.3190 (mt)
REVERT: A  112 ASP cc_start: 0.5680 (m-30) cc_final: 0.4767 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 372
  average time/residue: 0.2643
  time to fit residues: 135.0929
Evaluate side-chains
  251 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 111 optimal weight:    0.0670
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:    8.9990
   chunk 128 optimal weight:    0.4980
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
C  76 ASN
C 134 GLN
C 281 ASN
C 317 GLN
C 339 GLN
E  56 ASN
E  73 GLN
E 140 ASN
E 172 ASN
E 286 ASN
E 404 ASN
** F  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 137 HIS
D  69 ASN
D 141 HIS
D 152 GLN
D 204 HIS
** A  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 157 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.186031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.134469 restraints weight = 19531.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138004 restraints weight = 8974.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140112 restraints weight = 5665.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11161  Z= 0.112
  Angle     :  0.570  10.786  15104  Z= 0.286
  Chirality :  0.043   0.233   1742
  Planarity :  0.004   0.052   1950
  Dihedral  :  5.060  56.912   1579
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.68 %
    Favored  : 81.49 %
  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: -4.36 (0.17), residues: 1424
  helix: -3.28 (0.16), residues: 463
  sheet: -1.92 (0.36), residues: 187
  loop : -2.95 (0.18), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP E  75 
 HIS   0.009   0.001   HIS D 204 
 PHE   0.019   0.001   PHE D  68 
 TYR   0.012   0.001   TYR E 260 
 ARG   0.006   0.000   ARG E  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04996 (  275)
  hydrogen bonds       : angle       5.53327 (  786)
  covalent geometry    : bond        0.00253 (11159)
  covalent geometry    : angle       0.56954 (15104)
  Misc. bond           : bond        0.00007 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 287
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   15 ARG cc_start: 0.6535 (mmp80) cc_final: 0.5165 (pmt-80)
REVERT: C   63 MET cc_start: 0.8502 (tmm) cc_final: 0.8143 (tmm)
REVERT: C   75 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8420 (tp)
REVERT: E   75 TRP cc_start: 0.6895 (m100) cc_final: 0.6599 (m100)
REVERT: E  325 LEU cc_start: 0.8918 (mm) cc_final: 0.8539 (mt)
REVERT: F   73 MET cc_start: 0.4203 (ppp) cc_final: 0.3815 (ppp)
REVERT: F  106 GLU cc_start: 0.7438 (pt0) cc_final: 0.7049 (mt-10)
REVERT: D   51 LEU cc_start: 0.8566 (mt) cc_final: 0.8359 (mt)
REVERT: D   86 ASN cc_start: 0.7244 (p0) cc_final: 0.6664 (t0)
REVERT: D  142 ARG cc_start: 0.8255 (mmt-90) cc_final: 0.8046 (mmt90)
REVERT: D  171 GLU cc_start: 0.8115 (tt0) cc_final: 0.7822 (tm-30)
REVERT: A  112 ASP cc_start: 0.6025 (m-30) cc_final: 0.5187 (t0)
  outliers start: 21
  outliers final: 10
  residues processed: 299
  average time/residue: 0.2168
  time to fit residues: 93.0899
Evaluate side-chains
  248 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 237
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  157 ASN
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  149 ILE
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  358 HIS
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain D residue  152 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 106 optimal weight:    5.9990
   chunk 138 optimal weight:   20.0000
   chunk 89 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
C  76 ASN
E 172 ASN
** F  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 ASN
D  10 ASN
D  27 ASN
D  53 HIS
D 141 HIS
A  45 ASN
** A  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 103 GLN
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.172307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.114282 restraints weight = 19333.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.117502 restraints weight = 9535.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119401 restraints weight = 6330.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11161  Z= 0.202
  Angle     :  0.665   7.609  15104  Z= 0.336
  Chirality :  0.046   0.191   1742
  Planarity :  0.005   0.050   1950
  Dihedral  :  5.629  58.310   1579
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.64 %
    Favored  : 76.63 %
  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: -3.49 (0.19), residues: 1424
  helix: -2.02 (0.21), residues: 483
  sheet: -2.11 (0.35), residues: 195
  loop : -2.60 (0.19), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  28 
 HIS   0.004   0.001   HIS E 376 
 PHE   0.024   0.002   PHE D  68 
 TYR   0.017   0.002   TYR E 260 
 ARG   0.006   0.001   ARG D 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04627 (  275)
  hydrogen bonds       : angle       4.98753 (  786)
  covalent geometry    : bond        0.00474 (11159)
  covalent geometry    : angle       0.66485 (15104)
  Misc. bond           : bond        0.00068 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 249
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  165 MET cc_start: 0.7669 (ttp) cc_final: 0.7279 (ttm)
REVERT: C  231 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8354 (mttm)
REVERT: C  311 MET cc_start: 0.8420 (ttt) cc_final: 0.8084 (ttt)
REVERT: E    8 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6399 (mt)
REVERT: E   57 ASN cc_start: 0.8051 (p0) cc_final: 0.7752 (p0)
REVERT: E   75 TRP cc_start: 0.7085 (m100) cc_final: 0.6865 (m100)
REVERT: E  325 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8578 (mt)
REVERT: E  369 ASP cc_start: 0.7592 (t70) cc_final: 0.7227 (t0)
REVERT: F  117 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7749 (mmtt)
REVERT: F  121 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: F  128 GLU cc_start: 0.7636 (pp20) cc_final: 0.7410 (pp20)
REVERT: F  129 MET cc_start: 0.7326 (tpp) cc_final: 0.6933 (tpp)
REVERT: F  190 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: D   86 ASN cc_start: 0.7424 (p0) cc_final: 0.6899 (t0)
REVERT: D  142 ARG cc_start: 0.8425 (mmt-90) cc_final: 0.8162 (mmt90)
REVERT: D  171 GLU cc_start: 0.8395 (tt0) cc_final: 0.8175 (tt0)
  outliers start: 43
  outliers final: 25
  residues processed: 270
  average time/residue: 0.2105
  time to fit residues: 82.2176
Evaluate side-chains
  255 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 PHE
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain E residue    8 LEU
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  129 LEU
Chi-restraints excluded: chain E residue  148 ILE
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  358 HIS
Chi-restraints excluded: chain F residue   49 SER
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue  108 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 104 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   chunk 135 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0670
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
C 317 GLN
E 359 GLN
** F  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 ASN
D 141 HIS
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 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 = 0.4210 r_free = 0.4210 target = 0.175684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120816 restraints weight = 19301.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123534 restraints weight = 9929.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126714 restraints weight = 6016.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11161  Z= 0.097
  Angle     :  0.537   6.931  15104  Z= 0.268
  Chirality :  0.044   0.333   1742
  Planarity :  0.004   0.048   1950
  Dihedral  :  5.050  55.254   1579
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.89 %
    Favored  : 75.50 %
  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: -2.88 (0.20), residues: 1424
  helix: -1.15 (0.23), residues: 478
  sheet: -1.93 (0.36), residues: 186
  loop : -2.46 (0.19), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 138 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.026   0.001   PHE D  68 
 TYR   0.016   0.001   TYR E 260 
 ARG   0.003   0.000   ARG E  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 (  275)
  hydrogen bonds       : angle       4.57890 (  786)
  covalent geometry    : bond        0.00225 (11159)
  covalent geometry    : angle       0.53680 (15104)
  Misc. bond           : bond        0.00014 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 256
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.8567 (t80) cc_final: 0.8293 (t80)
REVERT: C   48 MET cc_start: 0.8032 (mtt) cc_final: 0.7774 (mtt)
REVERT: C   75 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8137 (tp)
REVERT: C  231 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8368 (mttm)
REVERT: C  311 MET cc_start: 0.8481 (ttt) cc_final: 0.8212 (ttt)
REVERT: E   57 ASN cc_start: 0.7965 (p0) cc_final: 0.7723 (p0)
REVERT: E   75 TRP cc_start: 0.7212 (m100) cc_final: 0.6823 (m100)
REVERT: E  203 PHE cc_start: 0.7768 (t80) cc_final: 0.7509 (t80)
REVERT: E  325 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8532 (mt)
REVERT: E  364 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8227 (t0)
REVERT: F  106 GLU cc_start: 0.7810 (pt0) cc_final: 0.7230 (mt-10)
REVERT: F  121 GLU cc_start: 0.8786 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: F  220 ASP cc_start: 0.7128 (t70) cc_final: 0.6789 (t0)
REVERT: D   38 MET cc_start: 0.4811 (mmp) cc_final: 0.4350 (mmp)
REVERT: D   86 ASN cc_start: 0.7495 (p0) cc_final: 0.6984 (t0)
REVERT: D  142 ARG cc_start: 0.8492 (mmt-90) cc_final: 0.8226 (mmt180)
  outliers start: 30
  outliers final: 13
  residues processed: 274
  average time/residue: 0.2069
  time to fit residues: 81.9159
Evaluate side-chains
  250 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 234
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  358 HIS
Chi-restraints excluded: chain E residue  364 ASP
Chi-restraints excluded: chain E residue  368 ILE
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain A residue   88 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 116 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0010
   chunk 85 optimal weight:    8.9990
   chunk 122 optimal weight:   30.0000
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.6992

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 ASN
D 141 HIS
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  50 HIS
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.171559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.113054 restraints weight = 19252.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.116413 restraints weight = 9235.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.118462 restraints weight = 6088.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11161  Z= 0.142
  Angle     :  0.578   7.769  15104  Z= 0.289
  Chirality :  0.045   0.341   1742
  Planarity :  0.004   0.055   1950
  Dihedral  :  5.151  56.443   1579
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.50 %
    Favored  : 74.63 %
  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: -2.51 (0.21), residues: 1424
  helix: -0.78 (0.23), residues: 496
  sheet: -1.74 (0.37), residues: 180
  loop : -2.31 (0.20), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 138 
 HIS   0.004   0.001   HIS F  96 
 PHE   0.021   0.001   PHE D  68 
 TYR   0.019   0.001   TYR E 260 
 ARG   0.004   0.000   ARG E 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  275)
  hydrogen bonds       : angle       4.57815 (  786)
  covalent geometry    : bond        0.00341 (11159)
  covalent geometry    : angle       0.57753 (15104)
  Misc. bond           : bond        0.00048 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 243
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: C  165 MET cc_start: 0.7824 (ttp) cc_final: 0.7464 (ttm)
REVERT: C  231 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8420 (mttm)
REVERT: E   57 ASN cc_start: 0.8169 (p0) cc_final: 0.7948 (p0)
REVERT: E   75 TRP cc_start: 0.7233 (m100) cc_final: 0.6943 (m100)
REVERT: E  261 MET cc_start: 0.8853 (tpp) cc_final: 0.8622 (tpp)
REVERT: E  325 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8536 (mt)
REVERT: E  400 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7140 (ttt180)
REVERT: F  106 GLU cc_start: 0.7759 (pt0) cc_final: 0.7353 (mp0)
REVERT: F  121 GLU cc_start: 0.8791 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: F  186 GLN cc_start: 0.7727 (pp30) cc_final: 0.7503 (pp30)
REVERT: F  187 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6845 (mm)
REVERT: F  190 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: F  205 ASP cc_start: 0.7660 (p0) cc_final: 0.7384 (p0)
REVERT: F  220 ASP cc_start: 0.6867 (t70) cc_final: 0.6613 (t0)
REVERT: D   38 MET cc_start: 0.4917 (mmp) cc_final: 0.4501 (mmp)
REVERT: D   86 ASN cc_start: 0.7487 (p0) cc_final: 0.7069 (t0)
REVERT: D  142 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8133 (mmt90)
  outliers start: 33
  outliers final: 22
  residues processed: 262
  average time/residue: 0.2110
  time to fit residues: 80.4629
Evaluate side-chains
  257 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue  129 LEU
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  193 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  358 HIS
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain A residue   88 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 130 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 105 optimal weight:   20.0000
   chunk 101 optimal weight:    0.0000
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   overall best weight:    1.3590

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 317 GLN
F 152 GLN
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.171453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.114816 restraints weight = 19289.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118630 restraints weight = 10160.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.119037 restraints weight = 6191.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.5437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11161  Z= 0.120
  Angle     :  0.564   7.809  15104  Z= 0.279
  Chirality :  0.044   0.290   1742
  Planarity :  0.004   0.053   1950
  Dihedral  :  5.185  59.482   1579
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.37 %
    Favored  : 73.24 %
  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 (0.21), residues: 1424
  helix: -0.28 (0.24), residues: 496
  sheet: -1.71 (0.36), residues: 181
  loop : -2.17 (0.21), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E 138 
 HIS   0.005   0.001   HIS F  96 
 PHE   0.022   0.001   PHE D  68 
 TYR   0.007   0.001   TYR A 104 
 ARG   0.002   0.000   ARG E  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03200 (  275)
  hydrogen bonds       : angle       4.47465 (  786)
  covalent geometry    : bond        0.00287 (11159)
  covalent geometry    : angle       0.56442 (15104)
  Misc. bond           : bond        0.00036 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 249
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6687 (tm-30)
REVERT: C  165 MET cc_start: 0.7750 (ttp) cc_final: 0.7404 (ttm)
REVERT: C  231 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8422 (mttm)
REVERT: E   12 ARG cc_start: 0.7745 (mmp80) cc_final: 0.7302 (mmp-170)
REVERT: E   57 ASN cc_start: 0.8248 (p0) cc_final: 0.8015 (p0)
REVERT: E   63 VAL cc_start: 0.9523 (t) cc_final: 0.9240 (m)
REVERT: E   75 TRP cc_start: 0.7357 (m100) cc_final: 0.6986 (m100)
REVERT: E  261 MET cc_start: 0.8765 (tpp) cc_final: 0.8516 (tpp)
REVERT: E  263 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7503 (ttm170)
REVERT: E  325 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8580 (mt)
REVERT: E  364 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8412 (t70)
REVERT: E  400 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7126 (ttt180)
REVERT: F   84 LEU cc_start: 0.7827 (pt) cc_final: 0.7574 (pp)
REVERT: F  121 GLU cc_start: 0.8788 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: F  185 PHE cc_start: 0.8554 (m-80) cc_final: 0.8248 (m-80)
REVERT: F  187 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7294 (mm)
REVERT: F  190 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: F  205 ASP cc_start: 0.7710 (p0) cc_final: 0.7370 (p0)
REVERT: F  218 MET cc_start: 0.6615 (tpt) cc_final: 0.6335 (tpt)
REVERT: F  220 ASP cc_start: 0.7092 (t70) cc_final: 0.6754 (t0)
REVERT: D   38 MET cc_start: 0.4849 (mmp) cc_final: 0.3208 (mmt)
REVERT: D   86 ASN cc_start: 0.7574 (p0) cc_final: 0.7204 (t0)
REVERT: D  142 ARG cc_start: 0.8539 (mmt-90) cc_final: 0.8183 (mmt90)
REVERT: D  171 GLU cc_start: 0.8233 (tt0) cc_final: 0.8022 (tt0)
  outliers start: 39
  outliers final: 24
  residues processed: 269
  average time/residue: 0.2089
  time to fit residues: 81.0047
Evaluate side-chains
  263 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 234
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  129 LEU
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  193 LEU
Chi-restraints excluded: chain E residue  263 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  358 HIS
Chi-restraints excluded: chain E residue  364 ASP
Chi-restraints excluded: chain E residue  371 LEU
Chi-restraints excluded: chain F residue   49 SER
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain D residue    8 CYS
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain A residue   88 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 127 optimal weight:   20.0000
   chunk 12 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 115 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 87 optimal weight:    0.6980
   chunk 99 optimal weight:    9.9990
   chunk 120 optimal weight:    5.9990
   chunk 126 optimal weight:    5.9990
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 ASN
D 162 ASN
** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.168931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110939 restraints weight = 19488.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.114070 restraints weight = 9493.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.115996 restraints weight = 6307.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.5848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11161  Z= 0.161
  Angle     :  0.615   7.681  15104  Z= 0.306
  Chirality :  0.046   0.285   1742
  Planarity :  0.004   0.058   1950
  Dihedral  :  5.427  57.251   1579
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 25.11 %
    Favored  : 71.50 %
  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: -1.99 (0.21), residues: 1424
  helix: -0.14 (0.24), residues: 498
  sheet: -1.76 (0.37), residues: 172
  loop : -2.07 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 138 
 HIS   0.007   0.001   HIS F  96 
 PHE   0.022   0.001   PHE D  68 
 TYR   0.009   0.001   TYR C 382 
 ARG   0.003   0.000   ARG D 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  275)
  hydrogen bonds       : angle       4.63585 (  786)
  covalent geometry    : bond        0.00385 (11159)
  covalent geometry    : angle       0.61536 (15104)
  Misc. bond           : bond        0.00051 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 238
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: C  138 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6987 (tm-30)
REVERT: C  231 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8485 (mttm)
REVERT: E   12 ARG cc_start: 0.8003 (mmp80) cc_final: 0.6839 (mmp80)
REVERT: E   75 TRP cc_start: 0.7174 (m100) cc_final: 0.6769 (m100)
REVERT: E  251 ILE cc_start: 0.8850 (mm) cc_final: 0.8561 (tt)
REVERT: E  261 MET cc_start: 0.8911 (tpp) cc_final: 0.8675 (tpp)
REVERT: E  263 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7496 (ttm170)
REVERT: E  325 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8569 (mt)
REVERT: E  364 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8590 (t70)
REVERT: E  400 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7216 (ttt180)
REVERT: F  121 GLU cc_start: 0.8761 (tm-30) cc_final: 0.7452 (tm-30)
REVERT: F  190 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: F  205 ASP cc_start: 0.7936 (p0) cc_final: 0.7609 (p0)
REVERT: F  220 ASP cc_start: 0.7083 (t70) cc_final: 0.6780 (t0)
REVERT: D   38 MET cc_start: 0.5109 (mmp) cc_final: 0.3725 (mmt)
REVERT: D   86 ASN cc_start: 0.7656 (p0) cc_final: 0.7220 (t0)
REVERT: D   87 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7876 (mm-40)
REVERT: D  171 GLU cc_start: 0.8303 (tt0) cc_final: 0.8094 (tt0)
  outliers start: 39
  outliers final: 26
  residues processed: 263
  average time/residue: 0.2141
  time to fit residues: 81.2087
Evaluate side-chains
  249 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 219
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  148 GLU
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  129 LEU
Chi-restraints excluded: chain E residue  134 GLN
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  263 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  358 HIS
Chi-restraints excluded: chain E residue  364 ASP
Chi-restraints excluded: chain E residue  371 LEU
Chi-restraints excluded: chain F residue   49 SER
Chi-restraints excluded: chain F residue  154 VAL
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain D residue    8 CYS
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain A residue   88 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 124 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 247 GLN
E 140 ASN
D  97 HIS
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  22 GLN
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.171163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115343 restraints weight = 19334.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.117340 restraints weight = 11752.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.118311 restraints weight = 7219.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.5900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11161  Z= 0.106
  Angle     :  0.583  14.855  15104  Z= 0.285
  Chirality :  0.045   0.318   1742
  Planarity :  0.004   0.051   1950
  Dihedral  :  5.258  59.942   1579
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.89 %
    Favored  : 71.42 %
  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: -1.74 (0.22), residues: 1424
  helix:  0.20 (0.25), residues: 491
  sheet: -1.67 (0.38), residues: 178
  loop : -2.00 (0.21), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP E 138 
 HIS   0.006   0.001   HIS F  96 
 PHE   0.025   0.001   PHE D  68 
 TYR   0.007   0.001   TYR A 104 
 ARG   0.002   0.000   ARG E  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03045 (  275)
  hydrogen bonds       : angle       4.47589 (  786)
  covalent geometry    : bond        0.00251 (11159)
  covalent geometry    : angle       0.58278 (15104)
  Misc. bond           : bond        0.00023 (    2)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 246
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
REVERT: C   63 MET cc_start: 0.8432 (tmm) cc_final: 0.8024 (tmm)
REVERT: C  138 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6946 (tm-30)
REVERT: C  231 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8392 (mttm)
REVERT: E   12 ARG cc_start: 0.8028 (mmp80) cc_final: 0.7659 (mmp-170)
REVERT: E   75 TRP cc_start: 0.7321 (m100) cc_final: 0.6837 (m100)
REVERT: E  251 ILE cc_start: 0.8831 (mm) cc_final: 0.8519 (tt)
REVERT: E  261 MET cc_start: 0.8731 (tpp) cc_final: 0.8512 (tpp)
REVERT: E  263 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7574 (ttm170)
REVERT: E  325 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8533 (mt)
REVERT: E  400 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7125 (ttt180)
REVERT: F  190 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7449 (tm-30)
REVERT: F  205 ASP cc_start: 0.7818 (p0) cc_final: 0.7509 (p0)
REVERT: F  220 ASP cc_start: 0.7487 (t70) cc_final: 0.7249 (t0)
REVERT: D   38 MET cc_start: 0.4990 (mmp) cc_final: 0.4355 (tpp)
REVERT: D   86 ASN cc_start: 0.7719 (p0) cc_final: 0.7277 (t0)
REVERT: D   87 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7703 (mm-40)
REVERT: D  142 ARG cc_start: 0.8556 (mmt180) cc_final: 0.7892 (mtt-85)
REVERT: D  212 MET cc_start: 0.6341 (pmm) cc_final: 0.3125 (ptt)
REVERT: A   22 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7108 (pp30)
REVERT: A  178 ASP cc_start: 0.7759 (t0) cc_final: 0.7448 (t0)
  outliers start: 31
  outliers final: 21
  residues processed: 265
  average time/residue: 0.2343
  time to fit residues: 89.7841
Evaluate side-chains
  261 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 236
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  129 LEU
Chi-restraints excluded: chain E residue  134 GLN
Chi-restraints excluded: chain E residue  188 HIS
Chi-restraints excluded: chain E residue  263 ARG
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue   12 CYS
Chi-restraints excluded: chain F residue   49 SER
Chi-restraints excluded: chain F residue  201 VAL
Chi-restraints excluded: chain D residue   95 PHE
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  141 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5211 > 50:
  distance: 66 - 81:  25.689
  distance: 78 - 81:  27.751
  distance: 79 - 102:  26.986
  distance: 81 - 82:  12.772
  distance: 82 - 83:  26.728
  distance: 82 - 85:  17.382
  distance: 83 - 84:  53.840
  distance: 83 - 89:  26.151
  distance: 84 - 110:  38.760
  distance: 85 - 86:  41.003
  distance: 85 - 87:  38.845
  distance: 89 - 90:   4.177
  distance: 90 - 91:  30.851
  distance: 90 - 93:  45.791
  distance: 91 - 92:  36.511
  distance: 91 - 94:  16.669
  distance: 94 - 95:  38.941
  distance: 95 - 96:  32.406
  distance: 95 - 98:  53.503
  distance: 96 - 97:  18.458
  distance: 99 - 100:  38.050
  distance: 99 - 101:  44.278
  distance: 102 - 103:  28.624
  distance: 103 - 104:  12.793
  distance: 103 - 106:  28.717
  distance: 104 - 105:   9.761
  distance: 104 - 110:  22.613
  distance: 106 - 107:  42.713
  distance: 107 - 108:  32.911
  distance: 107 - 109:  35.886
  distance: 110 - 111:  24.490
  distance: 111 - 112:  28.833
  distance: 111 - 114:  29.310
  distance: 112 - 113:  39.366
  distance: 112 - 116:  42.676
  distance: 114 - 115:  10.439
  distance: 116 - 117:  11.925
  distance: 117 - 118:  25.763
  distance: 117 - 120:  50.840
  distance: 118 - 119:   4.954
  distance: 118 - 123:  57.053
  distance: 119 - 150:  65.575
  distance: 123 - 124:   8.761
  distance: 124 - 125:  29.196
  distance: 124 - 127:  51.384
  distance: 125 - 126:  15.022
  distance: 125 - 131:  39.518
  distance: 126 - 156:  28.135
  distance: 127 - 128:  25.551
  distance: 128 - 129:   5.669
  distance: 128 - 130:  15.699
  distance: 131 - 132:  17.624
  distance: 132 - 133:  35.950
  distance: 132 - 135:  36.888
  distance: 133 - 134:  64.390
  distance: 133 - 143:  16.093
  distance: 135 - 136:  41.570
  distance: 136 - 137:  45.961
  distance: 136 - 138:  10.830
  distance: 137 - 139:  21.133
  distance: 138 - 140:  17.595
  distance: 139 - 141:  13.693
  distance: 140 - 141:  44.978
  distance: 141 - 142:  13.821
  distance: 143 - 144:   8.170
  distance: 143 - 149:  24.651
  distance: 144 - 145:  33.720
  distance: 144 - 147:   9.299
  distance: 145 - 146:  40.108
  distance: 145 - 150:  35.887
  distance: 147 - 148:  43.911
  distance: 148 - 149:  51.359
  distance: 150 - 151:  11.953
  distance: 151 - 152:  16.804
  distance: 151 - 154:  33.414
  distance: 152 - 153:  22.211
  distance: 152 - 156:  13.939
  distance: 153 - 176:  22.740
  distance: 154 - 155:  42.997