Starting phenix.real_space_refine
on Wed Mar  4 13:52:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6plo_20370/03_2026/6plo_20370.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6plo_20370/03_2026/6plo_20370.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6plo_20370/03_2026/6plo_20370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6plo_20370/03_2026/6plo_20370.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6plo_20370/03_2026/6plo_20370.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6plo_20370/03_2026/6plo_20370.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
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     100      5.16       5
     C    9230      2.51       5
     N    2275      2.21       5
     O    2560      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14165
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2787
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 329}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'ABU': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, G, H, I, J
  Time building chain proxies: 2.47, per 1000 atoms: 0.17
  Number of scatterers: 14165
  At special positions: 0
  Unit cell: (104.48, 105.786, 134.518, 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     100     16.00
     O    2560      8.00
     N    2275      7.00
     C    9230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS A 168 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 154 " - pdb=" SG  CYS B 168 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 154 " - pdb=" SG  CYS C 168 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 154 " - pdb=" SG  CYS D 168 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 154 " - pdb=" SG  CYS E 168 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS D 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 214 " - pdb=" SG  CYS E 225 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
    NAG-ASN
      " NAG F   1 " - " ASN A  54 "
      " NAG G   1 " - " ASN B  54 "
      " NAG H   1 " - " ASN C  54 "
      " NAG I   1 " - " ASN D  54 "
      " NAG J   1 " - " ASN E  54 "
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 682.1 milliseconds
  

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3320

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 25 sheets defined
      36.7% alpha, 39.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 35
      removed outlier: 3.656A  pdb=" N   LEU A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 90
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.579A  pdb=" N   LEU A 106 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP A 107 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 238 through 243
    Processing helix  chain 'A' and resid 243 through 255
      removed outlier: 3.573A  pdb=" N   SER A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE A 250 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TRP A 255 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 259
    Processing helix  chain 'A' and resid 266 through 285
      removed outlier: 3.691A  pdb=" N   GLY A 270 " --> pdb=" O   PRO A 266 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR A 275 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   MET A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN A 282 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 288
      No H-bonds generated for 'chain 'A' and resid 286 through 288'
    Processing helix  chain 'A' and resid 304 through 324
      removed outlier: 3.513A  pdb=" N   VAL A 310 " --> pdb=" O   CYS A 306 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA A 313 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LEU A 314 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE A 322 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 401
      removed outlier: 3.976A  pdb=" N   PHE A 395 " --> pdb=" O   MET A 391 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG A 401 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 428
      removed outlier: 3.566A  pdb=" N   PHE A 410 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      Proline residue:  A 411  - end of helix
      removed outlier: 4.199A  pdb=" N   LEU A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TRP A 422 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A 423 " --> pdb=" O   ILE A 419 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR A 425 " --> pdb=" O   TYR A 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 35
      removed outlier: 3.656A  pdb=" N   LEU B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 90
    Processing helix  chain 'B' and resid 102 through 107
      removed outlier: 3.580A  pdb=" N   LEU B 106 " --> pdb=" O   PRO B 103 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP B 107 " --> pdb=" O   SER B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 163
    Processing helix  chain 'B' and resid 238 through 243
    Processing helix  chain 'B' and resid 243 through 255
      removed outlier: 3.573A  pdb=" N   SER B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE B 250 " --> pdb=" O   PRO B 246 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL B 251 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   TRP B 255 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 259
    Processing helix  chain 'B' and resid 266 through 285
      removed outlier: 3.692A  pdb=" N   GLY B 270 " --> pdb=" O   PRO B 266 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR B 275 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL B 276 " --> pdb=" O   GLY B 272 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   MET B 279 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN B 282 " --> pdb=" O   THR B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 288
      No H-bonds generated for 'chain 'B' and resid 286 through 288'
    Processing helix  chain 'B' and resid 304 through 324
      removed outlier: 3.513A  pdb=" N   VAL B 310 " --> pdb=" O   CYS B 306 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA B 313 " --> pdb=" O   PHE B 309 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU B 314 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE B 322 " --> pdb=" O   ALA B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 401
      removed outlier: 3.975A  pdb=" N   PHE B 395 " --> pdb=" O   MET B 391 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE B 396 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER B 397 " --> pdb=" O   LYS B 393 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 401 " --> pdb=" O   SER B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 428
      removed outlier: 3.566A  pdb=" N   PHE B 410 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
      Proline residue:  B 411  - end of helix
      removed outlier: 4.199A  pdb=" N   LEU B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TRP B 422 " --> pdb=" O   ASN B 418 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 423 " --> pdb=" O   ILE B 419 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR B 425 " --> pdb=" O   TYR B 421 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 35
      removed outlier: 3.657A  pdb=" N   LEU C  33 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 90
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.580A  pdb=" N   LEU C 106 " --> pdb=" O   PRO C 103 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP C 107 " --> pdb=" O   SER C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 163
    Processing helix  chain 'C' and resid 238 through 243
    Processing helix  chain 'C' and resid 243 through 255
      removed outlier: 3.573A  pdb=" N   SER C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE C 250 " --> pdb=" O   PRO C 246 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL C 251 " --> pdb=" O   SER C 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TRP C 255 " --> pdb=" O   VAL C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 259
    Processing helix  chain 'C' and resid 266 through 285
      removed outlier: 3.691A  pdb=" N   GLY C 270 " --> pdb=" O   PRO C 266 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR C 275 " --> pdb=" O   LEU C 271 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL C 276 " --> pdb=" O   GLY C 272 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET C 279 " --> pdb=" O   THR C 275 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN C 282 " --> pdb=" O   THR C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 288
      No H-bonds generated for 'chain 'C' and resid 286 through 288'
    Processing helix  chain 'C' and resid 304 through 324
      removed outlier: 3.513A  pdb=" N   VAL C 310 " --> pdb=" O   CYS C 306 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA C 313 " --> pdb=" O   PHE C 309 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU C 314 " --> pdb=" O   VAL C 310 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE C 322 " --> pdb=" O   ALA C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 401
      removed outlier: 3.975A  pdb=" N   PHE C 395 " --> pdb=" O   MET C 391 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE C 396 " --> pdb=" O   ARG C 392 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER C 397 " --> pdb=" O   LYS C 393 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG C 401 " --> pdb=" O   SER C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 428
      removed outlier: 3.566A  pdb=" N   PHE C 410 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
      Proline residue:  C 411  - end of helix
      removed outlier: 4.198A  pdb=" N   LEU C 415 " --> pdb=" O   PRO C 411 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TRP C 422 " --> pdb=" O   ASN C 418 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR C 424 " --> pdb=" O   PHE C 420 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR C 425 " --> pdb=" O   TYR C 421 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 35
      removed outlier: 3.657A  pdb=" N   LEU D  33 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 90
    Processing helix  chain 'D' and resid 102 through 107
      removed outlier: 3.580A  pdb=" N   LEU D 106 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ASP D 107 " --> pdb=" O   SER D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 163
    Processing helix  chain 'D' and resid 238 through 243
    Processing helix  chain 'D' and resid 243 through 255
      removed outlier: 3.573A  pdb=" N   SER D 247 " --> pdb=" O   MET D 243 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE D 250 " --> pdb=" O   PRO D 246 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL D 251 " --> pdb=" O   SER D 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TRP D 255 " --> pdb=" O   VAL D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 259
    Processing helix  chain 'D' and resid 266 through 285
      removed outlier: 3.691A  pdb=" N   GLY D 270 " --> pdb=" O   PRO D 266 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR D 275 " --> pdb=" O   LEU D 271 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL D 276 " --> pdb=" O   GLY D 272 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   MET D 279 " --> pdb=" O   THR D 275 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN D 282 " --> pdb=" O   THR D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 288
      No H-bonds generated for 'chain 'D' and resid 286 through 288'
    Processing helix  chain 'D' and resid 304 through 324
      removed outlier: 3.513A  pdb=" N   VAL D 310 " --> pdb=" O   CYS D 306 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA D 313 " --> pdb=" O   PHE D 309 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU D 314 " --> pdb=" O   VAL D 310 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE D 322 " --> pdb=" O   ALA D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 401
      removed outlier: 3.975A  pdb=" N   PHE D 395 " --> pdb=" O   MET D 391 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE D 396 " --> pdb=" O   ARG D 392 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER D 397 " --> pdb=" O   LYS D 393 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG D 398 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG D 401 " --> pdb=" O   SER D 397 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 428
      removed outlier: 3.566A  pdb=" N   PHE D 410 " --> pdb=" O   SER D 406 " (cutoff:3.500A)
      Proline residue:  D 411  - end of helix
      removed outlier: 4.198A  pdb=" N   LEU D 415 " --> pdb=" O   PRO D 411 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TRP D 422 " --> pdb=" O   ASN D 418 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE D 423 " --> pdb=" O   ILE D 419 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR D 424 " --> pdb=" O   PHE D 420 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR D 425 " --> pdb=" O   TYR D 421 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 25 through 35
      removed outlier: 3.657A  pdb=" N   LEU E  33 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 90
    Processing helix  chain 'E' and resid 102 through 107
      removed outlier: 3.580A  pdb=" N   LEU E 106 " --> pdb=" O   PRO E 103 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ASP E 107 " --> pdb=" O   SER E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 163
    Processing helix  chain 'E' and resid 238 through 243
    Processing helix  chain 'E' and resid 243 through 255
      removed outlier: 3.572A  pdb=" N   SER E 247 " --> pdb=" O   MET E 243 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE E 250 " --> pdb=" O   PRO E 246 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL E 251 " --> pdb=" O   SER E 247 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TRP E 255 " --> pdb=" O   VAL E 251 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 256 through 259
    Processing helix  chain 'E' and resid 266 through 285
      removed outlier: 3.691A  pdb=" N   GLY E 270 " --> pdb=" O   PRO E 266 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR E 275 " --> pdb=" O   LEU E 271 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL E 276 " --> pdb=" O   GLY E 272 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET E 279 " --> pdb=" O   THR E 275 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN E 282 " --> pdb=" O   THR E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 286 through 288
      No H-bonds generated for 'chain 'E' and resid 286 through 288'
    Processing helix  chain 'E' and resid 304 through 324
      removed outlier: 3.512A  pdb=" N   VAL E 310 " --> pdb=" O   CYS E 306 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA E 313 " --> pdb=" O   PHE E 309 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LEU E 314 " --> pdb=" O   VAL E 310 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE E 322 " --> pdb=" O   ALA E 318 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 391 through 401
      removed outlier: 3.975A  pdb=" N   PHE E 395 " --> pdb=" O   MET E 391 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE E 396 " --> pdb=" O   ARG E 392 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER E 397 " --> pdb=" O   LYS E 393 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG E 398 " --> pdb=" O   LEU E 394 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG E 401 " --> pdb=" O   SER E 397 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 405 through 428
      removed outlier: 3.567A  pdb=" N   PHE E 410 " --> pdb=" O   SER E 406 " (cutoff:3.500A)
      Proline residue:  E 411  - end of helix
      removed outlier: 4.198A  pdb=" N   LEU E 415 " --> pdb=" O   PRO E 411 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TRP E 422 " --> pdb=" O   ASN E 418 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR E 424 " --> pdb=" O   PHE E 420 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR E 425 " --> pdb=" O   TYR E 421 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100
      removed outlier: 6.327A  pdb=" N   ASP A  73 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER A  66 " --> pdb=" O   ASP A  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE A  64 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN A  77 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ASN A  85 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASN A  54 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL A  53 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU A 185 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL A  55 " --> pdb=" O   GLU A 185 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123
      removed outlier: 6.327A  pdb=" N   ASP A  73 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER A  66 " --> pdb=" O   ASP A  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE A  64 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN A  77 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ASN A  85 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASN A  54 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLN A 193 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE A  59 " --> pdb=" O   GLN A 193 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116
    Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116
    Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217
    Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100
      removed outlier: 6.327A  pdb=" N   ASP B  73 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER B  66 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ARG B  75 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   PHE B  64 " --> pdb=" O   ARG B  75 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN B  77 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ASN B  85 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN B  54 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL B  53 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU B 185 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   VAL B  55 " --> pdb=" O   GLU B 185 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123
      removed outlier: 6.327A  pdb=" N   ASP B  73 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER B  66 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ARG B  75 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   PHE B  64 " --> pdb=" O   ARG B  75 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN B  77 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ASN B  85 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN B  54 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   GLN B 193 " --> pdb=" O   CYS B  57 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE B  59 " --> pdb=" O   GLN B 193 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116
    Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116
    Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217
    Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100
      removed outlier: 6.327A  pdb=" N   ASP C  73 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER C  66 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG C  75 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE C  64 " --> pdb=" O   ARG C  75 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ASN C  77 " --> pdb=" O   ASN C  62 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ASN C  85 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN C  54 " --> pdb=" O   ASN C  85 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL C  53 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU C 185 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL C  55 " --> pdb=" O   GLU C 185 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123
      removed outlier: 6.327A  pdb=" N   ASP C  73 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER C  66 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG C  75 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE C  64 " --> pdb=" O   ARG C  75 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ASN C  77 " --> pdb=" O   ASN C  62 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ASN C  85 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN C  54 " --> pdb=" O   ASN C  85 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLN C 193 " --> pdb=" O   CYS C  57 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE C  59 " --> pdb=" O   GLN C 193 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116
    Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116
    Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217
    Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100
      removed outlier: 6.326A  pdb=" N   ASP D  73 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER D  66 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG D  75 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   PHE D  64 " --> pdb=" O   ARG D  75 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN D  77 " --> pdb=" O   ASN D  62 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   ASN D  85 " --> pdb=" O   ASN D  54 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN D  54 " --> pdb=" O   ASN D  85 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL D  53 " --> pdb=" O   ILE D 183 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU D 185 " --> pdb=" O   VAL D  53 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL D  55 " --> pdb=" O   GLU D 185 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123
      removed outlier: 6.326A  pdb=" N   ASP D  73 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER D  66 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG D  75 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   PHE D  64 " --> pdb=" O   ARG D  75 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASN D  77 " --> pdb=" O   ASN D  62 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   ASN D  85 " --> pdb=" O   ASN D  54 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN D  54 " --> pdb=" O   ASN D  85 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLN D 193 " --> pdb=" O   CYS D  57 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE D  59 " --> pdb=" O   GLN D 193 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116
    Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116
    Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217
    Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100
      removed outlier: 6.327A  pdb=" N   ASP E  73 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER E  66 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG E  75 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE E  64 " --> pdb=" O   ARG E  75 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASN E  77 " --> pdb=" O   ASN E  62 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   ASN E  85 " --> pdb=" O   ASN E  54 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN E  54 " --> pdb=" O   ASN E  85 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL E  53 " --> pdb=" O   ILE E 183 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU E 185 " --> pdb=" O   VAL E  53 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL E  55 " --> pdb=" O   GLU E 185 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123
      removed outlier: 6.327A  pdb=" N   ASP E  73 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER E  66 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG E  75 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE E  64 " --> pdb=" O   ARG E  75 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASN E  77 " --> pdb=" O   ASN E  62 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   ASN E  85 " --> pdb=" O   ASN E  54 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN E  54 " --> pdb=" O   ASN E  85 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   GLN E 193 " --> pdb=" O   CYS E  57 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ILE E  59 " --> pdb=" O   GLN E 193 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116
    Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116
    Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217

    632 hydrogen bonds defined for protein.
    1806 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: 2.51

  Time building geometry restraints manager: 1.56 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: 4247
        1.34 -     1.46: 3535
        1.46 -     1.58: 6558
        1.58 -     1.70: 0
        1.70 -     1.83: 170
  Bond restraints: 14510
  Sorted by residual:
  bond pdb=" C1  BMA F   3 "
       pdb=" C2  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.554 -0.035 2.00e-02 2.50e+03 3.15e+00
  bond pdb=" C1  BMA H   3 "
       pdb=" C2  BMA H   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.554 -0.035 2.00e-02 2.50e+03 3.13e+00
  bond pdb=" C1  NAG I   2 "
       pdb=" O5  NAG I   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.12e+00
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.554 -0.035 2.00e-02 2.50e+03 3.07e+00
  bond pdb=" C1  NAG J   2 "
       pdb=" O5  NAG J   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.03e+00
  ... (remaining 14505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 18941
        2.40 -     4.81: 601
        4.81 -     7.21: 93
        7.21 -     9.62: 35
        9.62 -    12.02: 10
  Bond angle restraints: 19680
  Sorted by residual:
  angle pdb=" C   VAL A 127 "
        pdb=" N   THR A 128 "
        pdb=" CA  THR A 128 "
      ideal   model   delta    sigma   weight residual
     121.54  132.23  -10.69 1.91e+00 2.74e-01 3.13e+01
  angle pdb=" C   VAL D 127 "
        pdb=" N   THR D 128 "
        pdb=" CA  THR D 128 "
      ideal   model   delta    sigma   weight residual
     121.54  132.22  -10.68 1.91e+00 2.74e-01 3.12e+01
  angle pdb=" C   VAL C 127 "
        pdb=" N   THR C 128 "
        pdb=" CA  THR C 128 "
      ideal   model   delta    sigma   weight residual
     121.54  132.21  -10.67 1.91e+00 2.74e-01 3.12e+01
  angle pdb=" C   VAL B 127 "
        pdb=" N   THR B 128 "
        pdb=" CA  THR B 128 "
      ideal   model   delta    sigma   weight residual
     121.54  132.20  -10.66 1.91e+00 2.74e-01 3.12e+01
  angle pdb=" N   VAL E  37 "
        pdb=" CA  VAL E  37 "
        pdb=" C   VAL E  37 "
      ideal   model   delta    sigma   weight residual
     113.53  108.06    5.47 9.80e-01 1.04e+00 3.12e+01
  ... (remaining 19675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.71: 8625
       21.71 -    43.42: 185
       43.42 -    65.13: 10
       65.13 -    86.85: 35
       86.85 -   108.56: 20
  Dihedral angle restraints: 8875
    sinusoidal: 3760
      harmonic: 5115
  Sorted by residual:
  dihedral pdb=" CA  ASN D 261 "
           pdb=" C   ASN D 261 "
           pdb=" N   MET D 262 "
           pdb=" CA  MET D 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.85   28.15     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  ASN E 261 "
           pdb=" C   ASN E 261 "
           pdb=" N   MET E 262 "
           pdb=" CA  MET E 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.86   28.14     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  ASN B 261 "
           pdb=" C   ASN B 261 "
           pdb=" N   MET B 262 "
           pdb=" CA  MET B 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.86   28.14     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 8872 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1574
       0.055 -    0.110: 563
       0.110 -    0.165: 93
       0.165 -    0.220: 25
       0.220 -    0.276: 5
  Chirality restraints: 2260
  Sorted by residual:
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" C5  BMA I   3 "
            pdb=" C4  BMA I   3 "
            pdb=" C6  BMA I   3 "
            pdb=" O5  BMA I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 2257 not shown)

  Planarity restraints: 2440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 410 "    0.043 5.00e-02 4.00e+02   6.42e-02 6.59e+00
        pdb=" N   PRO A 411 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 411 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 411 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 410 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.58e+00
        pdb=" N   PRO C 411 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C 411 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 411 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 410 "   -0.043 5.00e-02 4.00e+02   6.39e-02 6.54e+00
        pdb=" N   PRO B 411 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 411 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 411 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2437 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 4548
        2.84 -     3.35: 12101
        3.35 -     3.87: 23166
        3.87 -     4.38: 27212
        4.38 -     4.90: 46095
  Nonbonded interactions: 113122
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C  69 "
            pdb=" NH2 ARG C 234 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OE2 GLU D  69 "
            pdb=" NH2 ARG D 234 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OE2 GLU A  69 "
            pdb=" NH2 ARG A 234 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OE2 GLU B  69 "
            pdb=" NH2 ARG B 234 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OE2 GLU E  69 "
            pdb=" NH2 ARG E 234 "
     model   vdw
     2.322 3.120
  ... (remaining 113117 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.280
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  14535  Z= 0.307
  Angle     :  1.069  12.024  19745  Z= 0.544
  Chirality :  0.058   0.276   2260
  Planarity :  0.007   0.064   2435
  Dihedral  : 12.903 108.558   5525
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.29 (0.14), residues: 1710
  helix: -4.71 (0.08), residues: 530
  sheet: -2.76 (0.23), residues: 345
  loop : -2.92 (0.17), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 234 
 TYR   0.024   0.003   TYR D 425 
 PHE   0.025   0.003   PHE C 115 
 TRP   0.015   0.002   TRP E 302 
 HIS   0.004   0.002   HIS E 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00732 (14510)
  covalent geometry    : angle       1.06335 (19680)
  SS BOND              : bond        0.00447 (   10)
  SS BOND              : angle       3.12885 (   20)
  hydrogen bonds       : bond        0.25781 (  487)
  hydrogen bonds       : angle      10.60289 ( 1806)
  link_BETA1-4         : bond        0.00469 (   10)
  link_BETA1-4         : angle       1.79973 (   30)
  link_NAG-ASN         : bond        0.00104 (    5)
  link_NAG-ASN         : angle       0.47896 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 441
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  156 MET cc_start: 0.8586 (mmm) cc_final: 0.8136 (mmm)
REVERT: A  426 LYS cc_start: 0.7044 (ttmt) cc_final: 0.6313 (mptt)
REVERT: B   63 SER cc_start: 0.8825 (t) cc_final: 0.8590 (m)
REVERT: B  113 ASP cc_start: 0.9085 (p0) cc_final: 0.8787 (p0)
REVERT: B  156 MET cc_start: 0.8611 (mmm) cc_final: 0.8079 (mmm)
REVERT: B  426 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6307 (mmtm)
REVERT: C  156 MET cc_start: 0.8607 (mmm) cc_final: 0.8149 (mmm)
REVERT: C  173 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7611 (mt-10)
REVERT: C  426 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6227 (mptt)
REVERT: D   43 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8801 (mtm180)
REVERT: D   63 SER cc_start: 0.8777 (t) cc_final: 0.8576 (m)
REVERT: D  156 MET cc_start: 0.8622 (mmm) cc_final: 0.8219 (mmm)
REVERT: D  426 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6244 (mmtm)
REVERT: E  156 MET cc_start: 0.8592 (mmm) cc_final: 0.8237 (mmm)
REVERT: E  426 LYS cc_start: 0.7023 (ttmt) cc_final: 0.6205 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 441
  average time/residue: 0.1225
  time to fit residues: 77.6058
Evaluate side-chains
  288 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.4980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
A 141 ASN
A 235 GLN
A 242 GLN
A 261 ASN
A 282 GLN
B  62 ASN
B 139 ASN
B 141 ASN
B 235 GLN
B 242 GLN
B 282 GLN
B 321 ASN
C  62 ASN
C 139 ASN
C 141 ASN
C 235 GLN
C 242 GLN
** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 282 GLN
D  62 ASN
D 139 ASN
D 141 ASN
D 231 HIS
D 235 GLN
D 242 GLN
D 282 GLN
E  62 ASN
E 139 ASN
E 141 ASN
E 231 HIS
E 235 GLN
E 242 GLN
E 261 ASN
E 282 GLN

Total number of N/Q/H flips: 34

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.163384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.126353 restraints weight = 17547.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.36
r_work: 0.3247 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14535  Z= 0.141
  Angle     :  0.716   6.323  19745  Z= 0.372
  Chirality :  0.047   0.173   2260
  Planarity :  0.005   0.039   2435
  Dihedral  : 10.792  68.112   2195
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 10.20 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.12 (0.16), residues: 1710
  helix: -3.50 (0.14), residues: 560
  sheet: -2.11 (0.24), residues: 350
  loop : -2.32 (0.19), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 147 
 TYR   0.015   0.001   TYR A 317 
 PHE   0.016   0.002   PHE E 203 
 TRP   0.010   0.001   TRP C  84 
 HIS   0.003   0.001   HIS E 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (14510)
  covalent geometry    : angle       0.70922 (19680)
  SS BOND              : bond        0.00468 (   10)
  SS BOND              : angle       1.55540 (   20)
  hydrogen bonds       : bond        0.04542 (  487)
  hydrogen bonds       : angle       5.83829 ( 1806)
  link_BETA1-4         : bond        0.00443 (   10)
  link_BETA1-4         : angle       2.41545 (   30)
  link_NAG-ASN         : bond        0.00097 (    5)
  link_NAG-ASN         : angle       0.47643 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 312
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  301 ILE cc_start: 0.8894 (pt) cc_final: 0.8572 (mt)
REVERT: A  317 TYR cc_start: 0.8593 (t80) cc_final: 0.8222 (t80)
REVERT: A  398 ARG cc_start: 0.6440 (mtt90) cc_final: 0.6177 (mmt-90)
REVERT: A  416 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8175 (pt)
REVERT: A  420 PHE cc_start: 0.8077 (t80) cc_final: 0.7242 (m-80)
REVERT: A  426 LYS cc_start: 0.6904 (ttmt) cc_final: 0.5750 (mmtm)
REVERT: B   63 SER cc_start: 0.9046 (t) cc_final: 0.8710 (m)
REVERT: B  204 ILE cc_start: 0.8867 (pt) cc_final: 0.8619 (pt)
REVERT: B  300 ASP cc_start: 0.8180 (m-30) cc_final: 0.7957 (m-30)
REVERT: B  301 ILE cc_start: 0.8894 (pt) cc_final: 0.8571 (mt)
REVERT: B  416 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8185 (pt)
REVERT: B  426 LYS cc_start: 0.7079 (ttmt) cc_final: 0.5906 (mmtm)
REVERT: C  301 ILE cc_start: 0.8867 (pt) cc_final: 0.8583 (mt)
REVERT: C  317 TYR cc_start: 0.8570 (t80) cc_final: 0.8169 (t80)
REVERT: C  398 ARG cc_start: 0.6394 (mtt90) cc_final: 0.6179 (mmt-90)
REVERT: C  416 ILE cc_start: 0.8355 (tp) cc_final: 0.8064 (pt)
REVERT: C  420 PHE cc_start: 0.8065 (t80) cc_final: 0.7303 (m-80)
REVERT: C  426 LYS cc_start: 0.6943 (ttmt) cc_final: 0.5763 (mmtm)
REVERT: D   43 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8676 (mtm180)
REVERT: D   63 SER cc_start: 0.9042 (t) cc_final: 0.8744 (m)
REVERT: D  301 ILE cc_start: 0.8848 (pt) cc_final: 0.8546 (mt)
REVERT: D  398 ARG cc_start: 0.6328 (mtt90) cc_final: 0.6092 (mmt-90)
REVERT: D  416 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8066 (pt)
REVERT: D  420 PHE cc_start: 0.8071 (t80) cc_final: 0.7186 (m-80)
REVERT: D  426 LYS cc_start: 0.7083 (ttmt) cc_final: 0.5909 (mmtm)
REVERT: E  301 ILE cc_start: 0.8876 (pt) cc_final: 0.8593 (mt)
REVERT: E  317 TYR cc_start: 0.8525 (t80) cc_final: 0.8272 (t80)
REVERT: E  416 ILE cc_start: 0.8382 (tp) cc_final: 0.8160 (pt)
REVERT: E  426 LYS cc_start: 0.6954 (ttmt) cc_final: 0.5704 (mmtt)
  outliers start: 42
  outliers final: 13
  residues processed: 331
  average time/residue: 0.1170
  time to fit residues: 56.6719
Evaluate side-chains
  309 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 293
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  227 GLU
Chi-restraints excluded: chain E residue  274 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 120 optimal weight:    4.9990
   chunk 154 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0010
   chunk 16 optimal weight:    0.5980
   chunk 133 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 137 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 231 HIS
B  62 ASN
B 231 HIS
B 261 ASN
B 321 ASN
C 231 HIS
C 242 GLN
C 261 ASN
D 242 GLN
D 261 ASN
E 242 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.166145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127274 restraints weight = 17594.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.58
r_work: 0.3255 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14535  Z= 0.115
  Angle     :  0.649   9.406  19745  Z= 0.329
  Chirality :  0.045   0.148   2260
  Planarity :  0.004   0.033   2435
  Dihedral  :  7.476  38.981   2195
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 11.37 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.17), residues: 1710
  helix: -2.38 (0.18), residues: 550
  sheet: -1.43 (0.25), residues: 345
  loop : -2.24 (0.19), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 147 
 TYR   0.016   0.001   TYR B 317 
 PHE   0.019   0.002   PHE E 322 
 TRP   0.011   0.001   TRP A  84 
 HIS   0.002   0.001   HIS B 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (14510)
  covalent geometry    : angle       0.64189 (19680)
  SS BOND              : bond        0.00346 (   10)
  SS BOND              : angle       1.43751 (   20)
  hydrogen bonds       : bond        0.03764 (  487)
  hydrogen bonds       : angle       4.75134 ( 1806)
  link_BETA1-4         : bond        0.00454 (   10)
  link_BETA1-4         : angle       2.30126 (   30)
  link_NAG-ASN         : bond        0.00056 (    5)
  link_NAG-ASN         : angle       0.46019 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 311
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  301 ILE cc_start: 0.8777 (pt) cc_final: 0.8522 (mt)
REVERT: A  314 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7350 (tt)
REVERT: A  398 ARG cc_start: 0.6340 (mtt90) cc_final: 0.6088 (mmt180)
REVERT: A  416 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8283 (pt)
REVERT: A  426 LYS cc_start: 0.6900 (ttmt) cc_final: 0.5772 (mmtm)
REVERT: B   63 SER cc_start: 0.8969 (t) cc_final: 0.8658 (m)
REVERT: B  204 ILE cc_start: 0.8880 (pt) cc_final: 0.8674 (pt)
REVERT: B  258 PHE cc_start: 0.8543 (m-80) cc_final: 0.8204 (m-80)
REVERT: B  300 ASP cc_start: 0.8011 (m-30) cc_final: 0.7792 (m-30)
REVERT: B  301 ILE cc_start: 0.8829 (pt) cc_final: 0.8534 (mt)
REVERT: B  416 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8152 (pt)
REVERT: B  420 PHE cc_start: 0.7902 (t80) cc_final: 0.7174 (m-80)
REVERT: B  426 LYS cc_start: 0.7134 (ttmt) cc_final: 0.5959 (mmtm)
REVERT: C  279 MET cc_start: 0.8734 (mmt) cc_final: 0.8433 (mmt)
REVERT: C  398 ARG cc_start: 0.6282 (mtt90) cc_final: 0.6008 (mmt180)
REVERT: C  426 LYS cc_start: 0.6932 (ttmt) cc_final: 0.5798 (mmtm)
REVERT: D   63 SER cc_start: 0.8980 (t) cc_final: 0.8730 (m)
REVERT: D  102 ASP cc_start: 0.7220 (p0) cc_final: 0.6836 (p0)
REVERT: D  159 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7248 (mmtt)
REVERT: D  301 ILE cc_start: 0.8701 (pt) cc_final: 0.8442 (mt)
REVERT: D  398 ARG cc_start: 0.6405 (mtt90) cc_final: 0.6019 (mmt180)
REVERT: D  416 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8143 (pt)
REVERT: D  426 LYS cc_start: 0.7091 (ttmt) cc_final: 0.5944 (mmtm)
REVERT: E  173 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: E  426 LYS cc_start: 0.6987 (ttmt) cc_final: 0.5819 (mmtm)
  outliers start: 60
  outliers final: 34
  residues processed: 343
  average time/residue: 0.1172
  time to fit residues: 58.2937
Evaluate side-chains
  322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 284
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  199 THR
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  316 GLU
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 131 optimal weight:    6.9990
   chunk 128 optimal weight:    0.5980
   chunk 151 optimal weight:    4.9990
   chunk 159 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   chunk 125 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 321 ASN
C 242 GLN
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.169585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134033 restraints weight = 17215.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.32
r_work: 0.3271 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14535  Z= 0.116
  Angle     :  0.624   9.385  19745  Z= 0.315
  Chirality :  0.045   0.137   2260
  Planarity :  0.004   0.028   2435
  Dihedral  :  5.882  30.054   2195
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 13.01 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.71 (0.18), residues: 1710
  helix: -1.77 (0.20), residues: 555
  sheet: -1.10 (0.26), residues: 350
  loop : -2.08 (0.19), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  75 
 TYR   0.012   0.001   TYR A 317 
 PHE   0.019   0.002   PHE A 322 
 TRP   0.011   0.001   TRP C 110 
 HIS   0.001   0.001   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (14510)
  covalent geometry    : angle       0.61831 (19680)
  SS BOND              : bond        0.00331 (   10)
  SS BOND              : angle       1.32437 (   20)
  hydrogen bonds       : bond        0.03288 (  487)
  hydrogen bonds       : angle       4.43227 ( 1806)
  link_BETA1-4         : bond        0.00436 (   10)
  link_BETA1-4         : angle       2.12376 (   30)
  link_NAG-ASN         : bond        0.00148 (    5)
  link_NAG-ASN         : angle       0.46474 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 288
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8870 (t80) cc_final: 0.8651 (t80)
REVERT: A  240 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8242 (mt)
REVERT: A  398 ARG cc_start: 0.6201 (mtt90) cc_final: 0.5917 (mmt180)
REVERT: A  414 PHE cc_start: 0.8473 (t80) cc_final: 0.8161 (t80)
REVERT: A  416 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8298 (pt)
REVERT: A  426 LYS cc_start: 0.6838 (ttmt) cc_final: 0.5787 (mmtm)
REVERT: B   63 SER cc_start: 0.9055 (t) cc_final: 0.8735 (m)
REVERT: B  300 ASP cc_start: 0.8179 (m-30) cc_final: 0.7861 (m-30)
REVERT: B  301 ILE cc_start: 0.8863 (pt) cc_final: 0.8585 (mt)
REVERT: B  416 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8140 (pt)
REVERT: B  420 PHE cc_start: 0.7962 (t80) cc_final: 0.7210 (m-80)
REVERT: B  426 LYS cc_start: 0.6985 (ttmt) cc_final: 0.5763 (mmtm)
REVERT: C  229 ARG cc_start: 0.9049 (mmt90) cc_final: 0.8837 (mtt-85)
REVERT: C  314 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7310 (tt)
REVERT: C  398 ARG cc_start: 0.6173 (mtt90) cc_final: 0.5942 (mmt180)
REVERT: C  426 LYS cc_start: 0.6903 (ttmt) cc_final: 0.5727 (mmtm)
REVERT: D   63 SER cc_start: 0.9036 (t) cc_final: 0.8766 (m)
REVERT: D  102 ASP cc_start: 0.7217 (p0) cc_final: 0.6915 (p0)
REVERT: D  159 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7247 (mmtt)
REVERT: D  240 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8318 (mt)
REVERT: D  398 ARG cc_start: 0.6240 (mtt90) cc_final: 0.5847 (mmt180)
REVERT: D  416 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8151 (pt)
REVERT: D  426 LYS cc_start: 0.6951 (ttmt) cc_final: 0.5738 (mmtm)
REVERT: E  173 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8315 (mt-10)
REVERT: E  426 LYS cc_start: 0.6934 (ttmt) cc_final: 0.5721 (mmtm)
  outliers start: 69
  outliers final: 50
  residues processed: 326
  average time/residue: 0.1225
  time to fit residues: 57.2783
Evaluate side-chains
  326 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 270
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  188 GLU
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  109 ILE
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  316 GLU
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue   32 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  199 THR
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  316 GLU
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 109 optimal weight:    8.9990
   chunk 86 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0570
   chunk 104 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 154 optimal weight:    0.0970
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.170875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.136038 restraints weight = 17112.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.26
r_work: 0.3314 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14535  Z= 0.103
  Angle     :  0.591   6.312  19745  Z= 0.300
  Chirality :  0.044   0.136   2260
  Planarity :  0.003   0.026   2435
  Dihedral  :  5.250  27.612   2195
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 14.71 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.19), residues: 1710
  helix: -1.33 (0.21), residues: 555
  sheet: -0.86 (0.26), residues: 350
  loop : -1.92 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  43 
 TYR   0.012   0.001   TYR D 317 
 PHE   0.041   0.002   PHE E 414 
 TRP   0.009   0.001   TRP C  84 
 HIS   0.001   0.000   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (14510)
  covalent geometry    : angle       0.58672 (19680)
  SS BOND              : bond        0.00273 (   10)
  SS BOND              : angle       1.21026 (   20)
  hydrogen bonds       : bond        0.03104 (  487)
  hydrogen bonds       : angle       4.17227 ( 1806)
  link_BETA1-4         : bond        0.00393 (   10)
  link_BETA1-4         : angle       1.74294 (   30)
  link_NAG-ASN         : bond        0.00151 (    5)
  link_NAG-ASN         : angle       0.38352 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 285
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8818 (t80) cc_final: 0.8607 (t80)
REVERT: A  204 ILE cc_start: 0.8894 (pt) cc_final: 0.8631 (tt)
REVERT: A  398 ARG cc_start: 0.6175 (mtt90) cc_final: 0.5928 (mmt180)
REVERT: A  414 PHE cc_start: 0.8415 (t80) cc_final: 0.8082 (t80)
REVERT: A  416 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8258 (pt)
REVERT: A  426 LYS cc_start: 0.6751 (ttmt) cc_final: 0.5714 (mmtm)
REVERT: B   63 SER cc_start: 0.9031 (t) cc_final: 0.8711 (m)
REVERT: B  300 ASP cc_start: 0.8191 (m-30) cc_final: 0.7830 (m-30)
REVERT: B  301 ILE cc_start: 0.8816 (pt) cc_final: 0.8579 (mt)
REVERT: B  416 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8165 (pt)
REVERT: B  426 LYS cc_start: 0.6907 (ttmt) cc_final: 0.5696 (mmtt)
REVERT: C  159 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7159 (mmmt)
REVERT: C  204 ILE cc_start: 0.8955 (pt) cc_final: 0.8714 (tt)
REVERT: C  227 GLU cc_start: 0.8845 (tt0) cc_final: 0.8302 (tt0)
REVERT: C  398 ARG cc_start: 0.6132 (mtt90) cc_final: 0.5915 (mmt180)
REVERT: C  426 LYS cc_start: 0.6852 (ttmt) cc_final: 0.5656 (mmtm)
REVERT: D   63 SER cc_start: 0.9017 (t) cc_final: 0.8731 (m)
REVERT: D  102 ASP cc_start: 0.7203 (p0) cc_final: 0.6638 (p0)
REVERT: D  159 LYS cc_start: 0.7633 (mtpt) cc_final: 0.7178 (mmtt)
REVERT: D  398 ARG cc_start: 0.6114 (mtt90) cc_final: 0.5780 (mmt180)
REVERT: D  416 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8136 (pt)
REVERT: D  426 LYS cc_start: 0.6843 (ttmt) cc_final: 0.5587 (mmtt)
REVERT: E  159 LYS cc_start: 0.7703 (mtpt) cc_final: 0.7223 (mmtt)
REVERT: E  173 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8027 (mt-10)
REVERT: E  418 ASN cc_start: 0.7990 (m-40) cc_final: 0.7571 (m110)
REVERT: E  426 LYS cc_start: 0.6867 (ttmt) cc_final: 0.5659 (mmtm)
  outliers start: 64
  outliers final: 54
  residues processed: 322
  average time/residue: 0.1291
  time to fit residues: 58.8977
Evaluate side-chains
  325 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 268
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   32 LYS
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  109 ILE
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  170 MET
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue   32 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  214 CYS
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  316 GLU
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 98 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.168374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.132968 restraints weight = 17173.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.31
r_work: 0.3254 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14535  Z= 0.128
  Angle     :  0.618   8.983  19745  Z= 0.311
  Chirality :  0.044   0.140   2260
  Planarity :  0.004   0.042   2435
  Dihedral  :  5.236  38.140   2195
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 14.64 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.19), residues: 1710
  helix: -1.14 (0.21), residues: 560
  sheet: -0.74 (0.27), residues: 350
  loop : -1.83 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  75 
 TYR   0.012   0.001   TYR E 317 
 PHE   0.024   0.002   PHE E 414 
 TRP   0.008   0.001   TRP E  84 
 HIS   0.003   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (14510)
  covalent geometry    : angle       0.61332 (19680)
  SS BOND              : bond        0.00346 (   10)
  SS BOND              : angle       1.61298 (   20)
  hydrogen bonds       : bond        0.03022 (  487)
  hydrogen bonds       : angle       4.20276 ( 1806)
  link_BETA1-4         : bond        0.00446 (   10)
  link_BETA1-4         : angle       1.63690 (   30)
  link_NAG-ASN         : bond        0.00172 (    5)
  link_NAG-ASN         : angle       0.50195 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 288
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8871 (t80) cc_final: 0.8645 (t80)
REVERT: A  204 ILE cc_start: 0.8909 (pt) cc_final: 0.8664 (tt)
REVERT: A  240 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8217 (mt)
REVERT: A  414 PHE cc_start: 0.8419 (t80) cc_final: 0.8111 (t80)
REVERT: A  416 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8293 (pt)
REVERT: A  426 LYS cc_start: 0.6746 (ttmt) cc_final: 0.5710 (mmtm)
REVERT: B   63 SER cc_start: 0.9059 (t) cc_final: 0.8746 (m)
REVERT: B  227 GLU cc_start: 0.8920 (tt0) cc_final: 0.8393 (tt0)
REVERT: B  300 ASP cc_start: 0.8197 (m-30) cc_final: 0.7820 (m-30)
REVERT: B  301 ILE cc_start: 0.8827 (pt) cc_final: 0.8581 (mt)
REVERT: B  416 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8146 (pt)
REVERT: B  420 PHE cc_start: 0.7826 (t80) cc_final: 0.7147 (m-80)
REVERT: B  426 LYS cc_start: 0.6891 (ttmt) cc_final: 0.5692 (mmtt)
REVERT: C  149 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8470 (m)
REVERT: C  159 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7235 (mmmt)
REVERT: C  204 ILE cc_start: 0.8946 (pt) cc_final: 0.8735 (tt)
REVERT: C  314 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7254 (tt)
REVERT: C  398 ARG cc_start: 0.6132 (mtt90) cc_final: 0.5915 (mmt180)
REVERT: C  426 LYS cc_start: 0.6854 (ttmt) cc_final: 0.5645 (mmtm)
REVERT: D   63 SER cc_start: 0.9083 (t) cc_final: 0.8766 (m)
REVERT: D  102 ASP cc_start: 0.7195 (p0) cc_final: 0.6785 (p0)
REVERT: D  159 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7240 (mmtt)
REVERT: D  240 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8247 (mt)
REVERT: D  398 ARG cc_start: 0.6043 (mtt90) cc_final: 0.5708 (mmt180)
REVERT: D  416 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (pt)
REVERT: D  426 LYS cc_start: 0.6863 (ttmt) cc_final: 0.5738 (mmtm)
REVERT: E  159 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7274 (mmtt)
REVERT: E  173 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8238 (mt-10)
REVERT: E  204 ILE cc_start: 0.8947 (pt) cc_final: 0.8740 (tt)
REVERT: E  426 LYS cc_start: 0.6878 (ttmt) cc_final: 0.5671 (mmtm)
  outliers start: 73
  outliers final: 57
  residues processed: 332
  average time/residue: 0.1181
  time to fit residues: 56.7770
Evaluate side-chains
  334 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 270
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  196 ASP
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   32 LYS
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  109 ILE
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  170 MET
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   32 LYS
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  108 SER
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  196 ASP
Chi-restraints excluded: chain E residue  199 THR
Chi-restraints excluded: chain E residue  214 CYS
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  316 GLU
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 138 optimal weight:    0.0980
   chunk 21 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    0.3980
   chunk 88 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.169502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.134657 restraints weight = 17068.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.26
r_work: 0.3293 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14535  Z= 0.108
  Angle     :  0.627  10.174  19745  Z= 0.311
  Chirality :  0.044   0.143   2260
  Planarity :  0.004   0.029   2435
  Dihedral  :  5.190  47.273   2195
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 15.03 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.19), residues: 1710
  helix: -0.91 (0.21), residues: 555
  sheet: -0.64 (0.27), residues: 350
  loop : -1.71 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  75 
 TYR   0.012   0.001   TYR E 317 
 PHE   0.021   0.002   PHE B 322 
 TRP   0.009   0.001   TRP C  84 
 HIS   0.002   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (14510)
  covalent geometry    : angle       0.61993 (19680)
  SS BOND              : bond        0.00410 (   10)
  SS BOND              : angle       2.37359 (   20)
  hydrogen bonds       : bond        0.02902 (  487)
  hydrogen bonds       : angle       4.11853 ( 1806)
  link_BETA1-4         : bond        0.00451 (   10)
  link_BETA1-4         : angle       1.55690 (   30)
  link_NAG-ASN         : bond        0.00186 (    5)
  link_NAG-ASN         : angle       0.39553 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 287
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8834 (t80) cc_final: 0.8586 (t80)
REVERT: A  159 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7262 (mmmt)
REVERT: A  204 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8631 (tt)
REVERT: A  240 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8189 (mt)
REVERT: A  314 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7143 (tt)
REVERT: A  416 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8284 (pt)
REVERT: A  426 LYS cc_start: 0.6752 (ttmt) cc_final: 0.5732 (mmtm)
REVERT: B   63 SER cc_start: 0.9027 (t) cc_final: 0.8705 (m)
REVERT: B  300 ASP cc_start: 0.8178 (m-30) cc_final: 0.7814 (m-30)
REVERT: B  301 ILE cc_start: 0.8814 (pt) cc_final: 0.8591 (mt)
REVERT: B  416 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8199 (pt)
REVERT: B  426 LYS cc_start: 0.6822 (ttmt) cc_final: 0.5777 (mmtm)
REVERT: C  149 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8486 (m)
REVERT: C  159 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7219 (mmmt)
REVERT: C  204 ILE cc_start: 0.8930 (pt) cc_final: 0.8715 (tt)
REVERT: C  314 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7208 (tt)
REVERT: C  398 ARG cc_start: 0.6137 (mtt90) cc_final: 0.5894 (mmt180)
REVERT: C  426 LYS cc_start: 0.6817 (ttmt) cc_final: 0.5613 (mmtm)
REVERT: D   63 SER cc_start: 0.9074 (t) cc_final: 0.8757 (m)
REVERT: D  102 ASP cc_start: 0.7176 (p0) cc_final: 0.6802 (p0)
REVERT: D  159 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7204 (mmtt)
REVERT: D  398 ARG cc_start: 0.5978 (mtt90) cc_final: 0.5687 (mmt180)
REVERT: D  416 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8120 (pt)
REVERT: D  418 ASN cc_start: 0.8184 (m-40) cc_final: 0.7966 (m110)
REVERT: D  426 LYS cc_start: 0.6808 (ttmt) cc_final: 0.5701 (mmtm)
REVERT: E  159 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7253 (mmtt)
REVERT: E  173 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8017 (mt-10)
REVERT: E  204 ILE cc_start: 0.8911 (pt) cc_final: 0.8706 (tt)
REVERT: E  426 LYS cc_start: 0.6841 (ttmt) cc_final: 0.5645 (mmtm)
  outliers start: 78
  outliers final: 57
  residues processed: 333
  average time/residue: 0.1203
  time to fit residues: 57.9576
Evaluate side-chains
  331 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 266
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   32 LYS
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  109 ILE
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  170 MET
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  196 ASP
Chi-restraints excluded: chain E residue  199 THR
Chi-restraints excluded: chain E residue  214 CYS
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0370
   chunk 115 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.163782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.125868 restraints weight = 17520.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.51
r_work: 0.3230 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14535  Z= 0.119
  Angle     :  0.640   8.816  19745  Z= 0.315
  Chirality :  0.044   0.143   2260
  Planarity :  0.004   0.035   2435
  Dihedral  :  5.177  46.214   2195
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 15.56 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.19), residues: 1710
  helix: -0.76 (0.21), residues: 555
  sheet: -0.51 (0.27), residues: 350
  loop : -1.63 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  75 
 TYR   0.012   0.001   TYR E 317 
 PHE   0.022   0.002   PHE E 322 
 TRP   0.008   0.001   TRP B 422 
 HIS   0.002   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (14510)
  covalent geometry    : angle       0.63356 (19680)
  SS BOND              : bond        0.00319 (   10)
  SS BOND              : angle       2.34428 (   20)
  hydrogen bonds       : bond        0.02883 (  487)
  hydrogen bonds       : angle       4.12882 ( 1806)
  link_BETA1-4         : bond        0.00458 (   10)
  link_BETA1-4         : angle       1.51271 (   30)
  link_NAG-ASN         : bond        0.00192 (    5)
  link_NAG-ASN         : angle       0.46707 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 278
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8799 (t80) cc_final: 0.8499 (t80)
REVERT: A  109 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8418 (tt)
REVERT: A  159 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7271 (mmmt)
REVERT: A  204 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8622 (tt)
REVERT: A  240 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8143 (mt)
REVERT: A  314 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7208 (tt)
REVERT: A  416 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8286 (pt)
REVERT: A  418 ASN cc_start: 0.8207 (m-40) cc_final: 0.7978 (m110)
REVERT: A  426 LYS cc_start: 0.6812 (ttmt) cc_final: 0.5786 (mmtm)
REVERT: B   63 SER cc_start: 0.8964 (t) cc_final: 0.8645 (m)
REVERT: B  300 ASP cc_start: 0.8022 (m-30) cc_final: 0.7729 (m-30)
REVERT: B  301 ILE cc_start: 0.8770 (pt) cc_final: 0.8551 (mt)
REVERT: B  416 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8206 (pt)
REVERT: B  426 LYS cc_start: 0.6888 (ttmt) cc_final: 0.5854 (mmtm)
REVERT: C  149 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8464 (m)
REVERT: C  159 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7279 (mmmt)
REVERT: C  204 ILE cc_start: 0.8919 (pt) cc_final: 0.8706 (tt)
REVERT: C  314 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7234 (tt)
REVERT: C  426 LYS cc_start: 0.6851 (ttmt) cc_final: 0.5669 (mmtm)
REVERT: D   63 SER cc_start: 0.9031 (t) cc_final: 0.8702 (m)
REVERT: D  159 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7210 (mmtt)
REVERT: D  240 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: D  398 ARG cc_start: 0.5927 (mtt90) cc_final: 0.5702 (mmt180)
REVERT: D  416 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8151 (pt)
REVERT: D  418 ASN cc_start: 0.8212 (m-40) cc_final: 0.8002 (m110)
REVERT: D  426 LYS cc_start: 0.6890 (ttmt) cc_final: 0.5804 (mmtm)
REVERT: E  159 LYS cc_start: 0.7703 (mtpt) cc_final: 0.7270 (mmtt)
REVERT: E  173 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7784 (mt-10)
REVERT: E  204 ILE cc_start: 0.8920 (pt) cc_final: 0.8698 (tt)
REVERT: E  426 LYS cc_start: 0.6902 (ttmt) cc_final: 0.5725 (mmtm)
  outliers start: 73
  outliers final: 57
  residues processed: 316
  average time/residue: 0.1163
  time to fit residues: 53.6462
Evaluate side-chains
  328 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 261
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  196 ASP
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   32 LYS
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  109 ILE
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  170 MET
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  196 ASP
Chi-restraints excluded: chain E residue  199 THR
Chi-restraints excluded: chain E residue  214 CYS
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 135 optimal weight:    0.9990
   chunk 131 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 162 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 152 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 242 GLN
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.158912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124532 restraints weight = 17534.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.40
r_work: 0.3177 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14535  Z= 0.209
  Angle     :  0.730   8.518  19745  Z= 0.360
  Chirality :  0.047   0.146   2260
  Planarity :  0.004   0.040   2435
  Dihedral  :  5.682  47.929   2195
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 15.62 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.19), residues: 1710
  helix: -0.81 (0.20), residues: 555
  sheet: -0.53 (0.28), residues: 350
  loop : -1.66 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  75 
 TYR   0.017   0.002   TYR B 175 
 PHE   0.031   0.002   PHE D 414 
 TRP   0.012   0.002   TRP B 422 
 HIS   0.002   0.001   HIS E 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (14510)
  covalent geometry    : angle       0.72362 (19680)
  SS BOND              : bond        0.00431 (   10)
  SS BOND              : angle       2.64231 (   20)
  hydrogen bonds       : bond        0.03258 (  487)
  hydrogen bonds       : angle       4.48221 ( 1806)
  link_BETA1-4         : bond        0.00545 (   10)
  link_BETA1-4         : angle       1.65259 (   30)
  link_NAG-ASN         : bond        0.00138 (    5)
  link_NAG-ASN         : angle       0.70181 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 275
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8668 (tt)
REVERT: A  314 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7224 (tt)
REVERT: A  416 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8300 (pt)
REVERT: A  426 LYS cc_start: 0.6825 (ttmt) cc_final: 0.5762 (mmtm)
REVERT: B   63 SER cc_start: 0.9066 (t) cc_final: 0.8721 (m)
REVERT: B  300 ASP cc_start: 0.8315 (m-30) cc_final: 0.7950 (m-30)
REVERT: B  301 ILE cc_start: 0.8844 (pt) cc_final: 0.8571 (mt)
REVERT: B  416 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8198 (pt)
REVERT: B  418 ASN cc_start: 0.8216 (m-40) cc_final: 0.7986 (m110)
REVERT: B  426 LYS cc_start: 0.6939 (ttmt) cc_final: 0.5755 (mmtm)
REVERT: C  149 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8518 (m)
REVERT: C  159 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7361 (mmmt)
REVERT: C  314 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7248 (tt)
REVERT: C  426 LYS cc_start: 0.6874 (ttmt) cc_final: 0.5716 (mmtm)
REVERT: D   63 SER cc_start: 0.9117 (t) cc_final: 0.8775 (m)
REVERT: D  102 ASP cc_start: 0.7308 (p0) cc_final: 0.6921 (p0)
REVERT: D  159 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7350 (mmtt)
REVERT: D  240 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8318 (mp)
REVERT: D  416 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8156 (pt)
REVERT: D  418 ASN cc_start: 0.8256 (m-40) cc_final: 0.8030 (m110)
REVERT: D  426 LYS cc_start: 0.6879 (ttmt) cc_final: 0.5691 (mmtm)
REVERT: E  173 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8303 (mt-10)
REVERT: E  426 LYS cc_start: 0.6935 (ttmt) cc_final: 0.5736 (mmtm)
  outliers start: 78
  outliers final: 57
  residues processed: 323
  average time/residue: 0.1211
  time to fit residues: 56.9878
Evaluate side-chains
  324 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 259
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   32 LYS
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  109 ILE
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  108 SER
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  188 GLU
Chi-restraints excluded: chain E residue  199 THR
Chi-restraints excluded: chain E residue  214 CYS
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 112 optimal weight:    4.9990
   chunk 168 optimal weight:    0.0040
   chunk 57 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 147 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0060
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.5408

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

Flipped N/Q/H residues before XYZ refinement:
D 242 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.163211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126896 restraints weight = 17422.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.32
r_work: 0.3218 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14535  Z= 0.111
  Angle     :  0.675   9.564  19745  Z= 0.327
  Chirality :  0.044   0.152   2260
  Planarity :  0.004   0.031   2435
  Dihedral  :  5.271  48.416   2195
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.45 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.19), residues: 1710
  helix: -0.57 (0.21), residues: 550
  sheet: -0.48 (0.28), residues: 340
  loop : -1.57 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  75 
 TYR   0.013   0.001   TYR E 317 
 PHE   0.032   0.002   PHE A 414 
 TRP   0.009   0.001   TRP C  84 
 HIS   0.002   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (14510)
  covalent geometry    : angle       0.67033 (19680)
  SS BOND              : bond        0.00362 (   10)
  SS BOND              : angle       2.14397 (   20)
  hydrogen bonds       : bond        0.02960 (  487)
  hydrogen bonds       : angle       4.19650 ( 1806)
  link_BETA1-4         : bond        0.00460 (   10)
  link_BETA1-4         : angle       1.51470 (   30)
  link_NAG-ASN         : bond        0.00206 (    5)
  link_NAG-ASN         : angle       0.35661 (   15)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 268
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 MET cc_start: 0.7013 (ptp) cc_final: 0.6623 (ptp)
REVERT: A  109 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8454 (tt)
REVERT: A  204 ILE cc_start: 0.8808 (pt) cc_final: 0.8583 (tt)
REVERT: A  314 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7143 (tt)
REVERT: A  416 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8258 (pt)
REVERT: A  426 LYS cc_start: 0.6732 (ttmt) cc_final: 0.5658 (mmtm)
REVERT: B   63 SER cc_start: 0.9056 (t) cc_final: 0.8736 (m)
REVERT: B  300 ASP cc_start: 0.8306 (m-30) cc_final: 0.7966 (m-30)
REVERT: B  416 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8158 (pt)
REVERT: B  418 ASN cc_start: 0.8183 (m-40) cc_final: 0.7928 (m110)
REVERT: B  426 LYS cc_start: 0.6873 (ttmt) cc_final: 0.5792 (mmtm)
REVERT: C  149 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8464 (m)
REVERT: C  159 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7308 (mmmt)
REVERT: C  314 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7213 (tt)
REVERT: C  426 LYS cc_start: 0.6850 (ttmt) cc_final: 0.5622 (mmtm)
REVERT: D   63 SER cc_start: 0.9090 (t) cc_final: 0.8781 (m)
REVERT: D  159 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7290 (mmtt)
REVERT: D  416 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8094 (pt)
REVERT: D  418 ASN cc_start: 0.8207 (m-40) cc_final: 0.7946 (m110)
REVERT: D  426 LYS cc_start: 0.6807 (ttmt) cc_final: 0.5712 (mmtm)
REVERT: E  159 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7298 (mmtt)
REVERT: E  173 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8269 (mt-10)
REVERT: E  426 LYS cc_start: 0.6857 (ttmt) cc_final: 0.5626 (mmtm)
  outliers start: 57
  outliers final: 46
  residues processed: 298
  average time/residue: 0.1172
  time to fit residues: 51.0937
Evaluate side-chains
  310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 257
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  109 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  415 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   32 LYS
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  146 ILE
Chi-restraints excluded: chain D residue  196 ASP
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  274 THR
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  415 LEU
Chi-restraints excluded: chain D residue  416 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  109 ILE
Chi-restraints excluded: chain E residue  214 CYS
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  274 THR
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  296 VAL
Chi-restraints excluded: chain E residue  415 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 145 optimal weight:    0.0370
   chunk 107 optimal weight:    5.9990
   chunk 127 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.1980
   chunk 155 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0370
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
D 242 GLN
E 242 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.165182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.129284 restraints weight = 17401.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.28
r_work: 0.3262 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14535  Z= 0.104
  Angle     :  0.659   8.848  19745  Z= 0.318
  Chirality :  0.044   0.157   2260
  Planarity :  0.004   0.033   2435
  Dihedral  :  5.028  45.874   2195
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.39 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.20), residues: 1710
  helix: -0.42 (0.22), residues: 550
  sheet:  0.06 (0.28), residues: 315
  loop : -1.44 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  75 
 TYR   0.013   0.001   TYR E 317 
 PHE   0.031   0.002   PHE B 414 
 TRP   0.010   0.001   TRP C  84 
 HIS   0.002   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (14510)
  covalent geometry    : angle       0.65444 (19680)
  SS BOND              : bond        0.00300 (   10)
  SS BOND              : angle       2.02413 (   20)
  hydrogen bonds       : bond        0.02826 (  487)
  hydrogen bonds       : angle       4.04327 ( 1806)
  link_BETA1-4         : bond        0.00461 (   10)
  link_BETA1-4         : angle       1.43439 (   30)
  link_NAG-ASN         : bond        0.00185 (    5)
  link_NAG-ASN         : angle       0.44337 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3618.50 seconds
wall clock time: 62 minutes 31.32 seconds (3751.32 seconds total)