Starting phenix.real_space_refine
on Tue Mar  3 18:20:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lze_23605/03_2026/7lze_23605.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lze_23605/03_2026/7lze_23605.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lze_23605/03_2026/7lze_23605.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lze_23605/03_2026/7lze_23605.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lze_23605/03_2026/7lze_23605.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lze_23605/03_2026/7lze_23605.map"
  }
  resolution = 3.23
  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=   0.006 sd=   0.091
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      69      5.16       5
     C    4899      2.51       5
     N    1314      2.21       5
     O    1560      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 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: 7842
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2572
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 12, 'TRANS': 324}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2572
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 12, 'TRANS': 324}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2572
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 12, 'TRANS': 324}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.85, per 1000 atoms: 0.24
  Number of scatterers: 7842
  At special positions: 0
  Unit cell: (88.7841, 86.5919, 107.418, 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      69     16.00
     O    1560      8.00
     N    1314      7.00
     C    4899      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 182 " - pdb=" SG  CYS C 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 283 " - pdb=" SG  CYS A 311 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 292 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 390 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 188 " - pdb=" SG  CYS C 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 283 " - pdb=" SG  CYS B 311 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 292 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 384 " - pdb=" SG  CYS B 390 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  28 " - pdb=" SG  CYS C 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 283 " - pdb=" SG  CYS C 311 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 292 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 384 " - pdb=" SG  CYS C 390 " 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 D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A  57 "
      " NAG B 601 " - " ASN B  57 "
      " NAG C 601 " - " ASN C  57 "
      " NAG D   1 " - " ASN A 353 "
      " NAG E   1 " - " ASN B 353 "
      " NAG F   1 " - " ASN C 353 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 279.3 milliseconds
  

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 16 sheets defined
      25.1% alpha, 28.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 84
      removed outlier: 3.716A  pdb=" N   GLU A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR A  83 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   VAL A  84 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 197
      removed outlier: 3.545A  pdb=" N   MET A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.593A  pdb=" N   LEU A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 233
    Processing helix  chain 'A' and resid 237 through 247
    Processing helix  chain 'A' and resid 248 through 253
      removed outlier: 3.681A  pdb=" N   ARG A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 248 through 253'
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 4.166A  pdb=" N   ILE A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 84
      removed outlier: 3.990A  pdb=" N   THR B  83 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL B  84 " --> pdb=" O   GLU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 197
      removed outlier: 3.555A  pdb=" N   SER B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 211
      removed outlier: 3.871A  pdb=" N   LEU B 201 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 233
    Processing helix  chain 'B' and resid 237 through 247
    Processing helix  chain 'B' and resid 248 through 255
      removed outlier: 3.585A  pdb=" N   ARG B 252 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 4.028A  pdb=" N   ILE B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 84
      removed outlier: 3.649A  pdb=" N   GLU C  70 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   THR C  83 " --> pdb=" O   ARG C  79 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   VAL C  84 " --> pdb=" O   GLU C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 197
      removed outlier: 3.639A  pdb=" N   SER C 194 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 211
      removed outlier: 3.643A  pdb=" N   LEU C 201 " --> pdb=" O   ASN C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 233
    Processing helix  chain 'C' and resid 237 through 247
    Processing helix  chain 'C' and resid 248 through 253
      removed outlier: 3.718A  pdb=" N   ARG C 252 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG C 253 " --> pdb=" O   ALA C 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 248 through 253'
    Processing helix  chain 'C' and resid 348 through 353
      removed outlier: 4.118A  pdb=" N   ILE C 352 " --> pdb=" O   ARG C 348 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24
      removed outlier: 4.231A  pdb=" N   GLY A  34 " --> pdb=" O   CYS A 283 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   CYS A 283 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   LEU A  36 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   THR A 281 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL A  38 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ILE A 279 " --> pdb=" O   VAL A  38 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   ARG A  40 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   GLY A 277 " --> pdb=" O   ARG A  40 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   GLY A  42 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A 275 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LYS A 312 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 263
      removed outlier: 7.080A  pdb=" N   ILE A 268 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   VAL A 262 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   SER A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL A  47 " --> pdb=" O   HIS C 435 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   ILE C 437 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   THR A  49 " --> pdb=" O   ILE C 437 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295
      removed outlier: 3.514A  pdb=" N   SER A 291 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU A 303 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 376
      removed outlier: 3.928A  pdb=" N   CYS A 384 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY A 406 " --> pdb=" O   CYS A 384 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 393
    Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 438
      removed outlier: 6.911A  pdb=" N   SER B 266 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   VAL B 262 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ILE B 268 " --> pdb=" O   ILE B 260 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 21 through 24
      removed outlier: 4.007A  pdb=" N   GLY B  34 " --> pdb=" O   CYS B 283 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   CYS B 283 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   LEU B  36 " --> pdb=" O   THR B 281 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   THR B 281 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   VAL B  38 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ILE B 279 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ARG B  40 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   GLY B 277 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLY B  42 " --> pdb=" O   ILE B 275 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ILE B 275 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   LYS B 312 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 24
      removed outlier: 8.181A  pdb=" N   VAL B 333 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU B  36 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU B 327 " --> pdb=" O   PHE B 334 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 291 through 294
      removed outlier: 3.702A  pdb=" N   ALA B 300 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B 303 " --> pdb=" O   SER B 364 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 376
      removed outlier: 3.798A  pdb=" N   CYS B 384 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY B 406 " --> pdb=" O   CYS B 384 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 401 through 402
      removed outlier: 3.912A  pdb=" N   LYS B 401 " --> pdb=" O   ILE B 392 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B 391 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 434 through 438
      removed outlier: 6.959A  pdb=" N   SER C 266 " --> pdb=" O   VAL C 262 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   VAL C 262 " --> pdb=" O   SER C 266 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE C 268 " --> pdb=" O   ILE C 260 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY C 257 " --> pdb=" O   THR C 214 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 24
      removed outlier: 4.236A  pdb=" N   GLY C  34 " --> pdb=" O   CYS C 283 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   CYS C 283 " --> pdb=" O   GLY C  34 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   LEU C  36 " --> pdb=" O   THR C 281 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   THR C 281 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL C  38 " --> pdb=" O   ILE C 279 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE C 279 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   ARG C  40 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   GLY C 277 " --> pdb=" O   ARG C  40 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLY C  42 " --> pdb=" O   ILE C 275 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE C 275 " --> pdb=" O   GLY C  42 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LYS C 312 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 291 through 295
      removed outlier: 3.506A  pdb=" N   SER C 291 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU C 303 " --> pdb=" O   SER C 364 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 376
      removed outlier: 3.952A  pdb=" N   CYS C 384 " --> pdb=" O   GLY C 406 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY C 406 " --> pdb=" O   CYS C 384 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 390 through 393

    293 hydrogen bonds defined for protein.
    807 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.12

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2565
        1.35 -     1.47: 1823
        1.47 -     1.59: 3487
        1.59 -     1.72: 0
        1.72 -     1.84: 90
  Bond restraints: 7965
  Sorted by residual:
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.03e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.95e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.92e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.83e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.80e+00
  ... (remaining 7960 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 10425
        1.04 -     2.08: 285
        2.08 -     3.12: 66
        3.12 -     4.17: 21
        4.17 -     5.21: 3
  Bond angle restraints: 10800
  Sorted by residual:
  angle pdb=" CA  CYS C 283 "
        pdb=" CB  CYS C 283 "
        pdb=" SG  CYS C 283 "
      ideal   model   delta    sigma   weight residual
     114.40  119.61   -5.21 2.30e+00 1.89e-01 5.13e+00
  angle pdb=" CA  CYS A 283 "
        pdb=" CB  CYS A 283 "
        pdb=" SG  CYS A 283 "
      ideal   model   delta    sigma   weight residual
     114.40  119.55   -5.15 2.30e+00 1.89e-01 5.00e+00
  angle pdb=" C   SER A 355 "
        pdb=" N   THR A 356 "
        pdb=" CA  THR A 356 "
      ideal   model   delta    sigma   weight residual
     121.54  125.17   -3.63 1.91e+00 2.74e-01 3.61e+00
  angle pdb=" C   SER C 355 "
        pdb=" N   THR C 356 "
        pdb=" CA  THR C 356 "
      ideal   model   delta    sigma   weight residual
     121.54  125.12   -3.58 1.91e+00 2.74e-01 3.52e+00
  angle pdb=" C   SER B 355 "
        pdb=" N   THR B 356 "
        pdb=" CA  THR B 356 "
      ideal   model   delta    sigma   weight residual
     121.54  125.06   -3.52 1.91e+00 2.74e-01 3.40e+00
  ... (remaining 10795 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 4494
       17.13 -    34.27: 369
       34.27 -    51.40: 127
       51.40 -    68.53: 21
       68.53 -    85.67: 11
  Dihedral angle restraints: 5022
    sinusoidal: 2091
      harmonic: 2931
  Sorted by residual:
  dihedral pdb=" CB  CYS B  60 "
           pdb=" SG  CYS B  60 "
           pdb=" SG  CYS B  63 "
           pdb=" CB  CYS B  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.67   85.67     1      1.00e+01 1.00e-02 8.87e+01
  dihedral pdb=" CB  CYS C  60 "
           pdb=" SG  CYS C  60 "
           pdb=" SG  CYS C  63 "
           pdb=" CB  CYS C  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.91  -79.91     1      1.00e+01 1.00e-02 7.92e+01
  dihedral pdb=" CB  CYS A  60 "
           pdb=" SG  CYS A  60 "
           pdb=" SG  CYS A  63 "
           pdb=" CB  CYS A  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.51  -79.51     1      1.00e+01 1.00e-02 7.85e+01
  ... (remaining 5019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 848
       0.032 -    0.063: 279
       0.063 -    0.095: 66
       0.095 -    0.127: 94
       0.127 -    0.158: 6
  Chirality restraints: 1293
  Sorted by residual:
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A  57 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.25e-01
  chirality pdb=" CA  VAL C  38 "
            pdb=" N   VAL C  38 "
            pdb=" C   VAL C  38 "
            pdb=" CB  VAL C  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE A 285 "
            pdb=" N   ILE A 285 "
            pdb=" C   ILE A 285 "
            pdb=" CB  ILE A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 1290 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 355 "    0.004 2.00e-02 2.50e+03   8.38e-03 7.02e-01
        pdb=" C   SER B 355 "   -0.014 2.00e-02 2.50e+03
        pdb=" O   SER B 355 "    0.005 2.00e-02 2.50e+03
        pdb=" N   THR B 356 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 355 "    0.004 2.00e-02 2.50e+03   8.30e-03 6.89e-01
        pdb=" C   SER C 355 "   -0.014 2.00e-02 2.50e+03
        pdb=" O   SER C 355 "    0.005 2.00e-02 2.50e+03
        pdb=" N   THR C 356 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 355 "    0.004 2.00e-02 2.50e+03   8.20e-03 6.73e-01
        pdb=" C   SER A 355 "   -0.014 2.00e-02 2.50e+03
        pdb=" O   SER A 355 "    0.005 2.00e-02 2.50e+03
        pdb=" N   THR A 356 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1072
        2.76 -     3.29: 7484
        3.29 -     3.83: 11854
        3.83 -     4.36: 14177
        4.36 -     4.90: 26051
  Nonbonded interactions: 60638
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 206 "
            pdb=" OG  SER A 218 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE1 GLN C 206 "
            pdb=" OG  SER C 218 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE2 GLU B 305 "
            pdb=" OG  SER B 364 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OE2 GLU C 305 "
            pdb=" OG  SER C 364 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OE1 GLN B 206 "
            pdb=" OG  SER B 218 "
     model   vdw
     2.302 3.040
  ... (remaining 60633 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.150
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7998  Z= 0.130
  Angle     :  0.458   5.208  10875  Z= 0.243
  Chirality :  0.043   0.158   1293
  Planarity :  0.002   0.020   1368
  Dihedral  : 13.958  82.348   3066
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.77 %
  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: -0.70 (0.28), residues: 999
  helix:  2.96 (0.38), residues: 225
  sheet: -1.15 (0.32), residues: 285
  loop : -1.74 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.008   0.001   TYR A 310 
 PHE   0.003   0.000   PHE A 334 
 TRP   0.002   0.000   TRP A  43 
 HIS   0.001   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7965)
  covalent geometry    : angle       0.45284 (10800)
  SS BOND              : bond        0.00330 (   24)
  SS BOND              : angle       0.93719 (   48)
  hydrogen bonds       : bond        0.25335 (  289)
  hydrogen bonds       : angle       8.45432 (  807)
  link_BETA1-4         : bond        0.00294 (    3)
  link_BETA1-4         : angle       0.80386 (    9)
  link_NAG-ASN         : bond        0.00157 (    6)
  link_NAG-ASN         : angle       1.09301 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: C  189 MET cc_start: 0.7566 (mtt) cc_final: 0.6877 (mtt)
REVERT: C  270 MET cc_start: 0.7362 (ttm) cc_final: 0.7162 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0600
  time to fit residues: 5.0166
Evaluate side-chains
  39 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0050
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.9998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.118233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.098460 restraints weight = 11683.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.67
r_work: 0.3173 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.0920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7998  Z= 0.157
  Angle     :  0.586   9.413  10875  Z= 0.306
  Chirality :  0.046   0.193   1293
  Planarity :  0.003   0.020   1368
  Dihedral  :  6.668  55.028   1281
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  5.04 %
    Favored  : 94.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.77 (0.27), residues: 999
  helix:  2.42 (0.35), residues: 231
  sheet: -0.93 (0.32), residues: 294
  loop : -1.75 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 248 
 TYR   0.018   0.001   TYR B 319 
 PHE   0.005   0.001   PHE B 200 
 TRP   0.006   0.001   TRP A 309 
 HIS   0.002   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7965)
  covalent geometry    : angle       0.57713 (10800)
  SS BOND              : bond        0.00609 (   24)
  SS BOND              : angle       1.29655 (   48)
  hydrogen bonds       : bond        0.04623 (  289)
  hydrogen bonds       : angle       5.70839 (  807)
  link_BETA1-4         : bond        0.00251 (    3)
  link_BETA1-4         : angle       1.13491 (    9)
  link_NAG-ASN         : bond        0.00768 (    6)
  link_NAG-ASN         : angle       1.52983 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7016 (m-40)
  outliers start: 4
  outliers final: 1
  residues processed: 53
  average time/residue: 0.0605
  time to fit residues: 4.9650
Evaluate side-chains
  40 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain C residue   58 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 90 optimal weight:    0.2980
   chunk 33 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0170
   chunk 55 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.7620

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.118094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.098455 restraints weight = 11711.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.67
r_work: 0.3169 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7998  Z= 0.127
  Angle     :  0.547   9.576  10875  Z= 0.284
  Chirality :  0.045   0.224   1293
  Planarity :  0.003   0.023   1368
  Dihedral  :  6.384  54.522   1281
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.93 %
    Favored  : 90.03 %
  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: -0.72 (0.27), residues: 999
  helix:  2.36 (0.35), residues: 231
  sheet: -0.87 (0.32), residues: 294
  loop : -1.70 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 367 
 TYR   0.018   0.001   TYR C 319 
 PHE   0.005   0.001   PHE B 200 
 TRP   0.003   0.001   TRP A 309 
 HIS   0.002   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7965)
  covalent geometry    : angle       0.53886 (10800)
  SS BOND              : bond        0.00597 (   24)
  SS BOND              : angle       1.30328 (   48)
  hydrogen bonds       : bond        0.03805 (  289)
  hydrogen bonds       : angle       5.18054 (  807)
  link_BETA1-4         : bond        0.00450 (    3)
  link_BETA1-4         : angle       1.26741 (    9)
  link_NAG-ASN         : bond        0.00611 (    6)
  link_NAG-ASN         : angle       1.22054 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8962 (mtm) cc_final: 0.8668 (mtm)
REVERT: B   57 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.6882 (m-40)
  outliers start: 9
  outliers final: 3
  residues processed: 52
  average time/residue: 0.0612
  time to fit residues: 4.9886
Evaluate side-chains
  46 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain C residue  410 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 61 optimal weight:    0.2980
   chunk 59 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.118378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.098778 restraints weight = 11707.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.66
r_work: 0.3179 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7998  Z= 0.116
  Angle     :  0.547   9.725  10875  Z= 0.284
  Chirality :  0.045   0.238   1293
  Planarity :  0.003   0.022   1368
  Dihedral  :  6.215  55.029   1281
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.62 %
    Favored  : 88.89 %
  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: -0.68 (0.27), residues: 999
  helix:  2.37 (0.35), residues: 231
  sheet: -0.66 (0.33), residues: 279
  loop : -1.77 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 367 
 TYR   0.021   0.001   TYR B 319 
 PHE   0.004   0.001   PHE B 256 
 TRP   0.002   0.000   TRP A 284 
 HIS   0.002   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7965)
  covalent geometry    : angle       0.53834 (10800)
  SS BOND              : bond        0.00609 (   24)
  SS BOND              : angle       1.32157 (   48)
  hydrogen bonds       : bond        0.03362 (  289)
  hydrogen bonds       : angle       4.85920 (  807)
  link_BETA1-4         : bond        0.00381 (    3)
  link_BETA1-4         : angle       1.23876 (    9)
  link_NAG-ASN         : bond        0.00534 (    6)
  link_NAG-ASN         : angle       1.31081 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8945 (mtm) cc_final: 0.8648 (mtm)
REVERT: C  319 TYR cc_start: 0.8541 (t80) cc_final: 0.8321 (t80)
  outliers start: 13
  outliers final: 12
  residues processed: 53
  average time/residue: 0.0493
  time to fit residues: 4.4448
Evaluate side-chains
  52 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain C residue  417 THR
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.117239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.097741 restraints weight = 11759.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.65
r_work: 0.3163 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7998  Z= 0.132
  Angle     :  0.549   9.702  10875  Z= 0.284
  Chirality :  0.045   0.237   1293
  Planarity :  0.003   0.023   1368
  Dihedral  :  6.144  54.841   1281
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.42 %
    Favored  : 87.74 %
  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: -0.73 (0.27), residues: 999
  helix:  2.37 (0.35), residues: 231
  sheet: -0.66 (0.33), residues: 279
  loop : -1.85 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 253 
 TYR   0.024   0.001   TYR B 319 
 PHE   0.005   0.001   PHE B 256 
 TRP   0.003   0.001   TRP A 284 
 HIS   0.002   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7965)
  covalent geometry    : angle       0.53878 (10800)
  SS BOND              : bond        0.00605 (   24)
  SS BOND              : angle       1.34527 (   48)
  hydrogen bonds       : bond        0.03355 (  289)
  hydrogen bonds       : angle       4.73108 (  807)
  link_BETA1-4         : bond        0.00457 (    3)
  link_BETA1-4         : angle       1.25757 (    9)
  link_NAG-ASN         : bond        0.00378 (    6)
  link_NAG-ASN         : angle       1.51068 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8972 (mtm) cc_final: 0.8663 (mtm)
  outliers start: 16
  outliers final: 13
  residues processed: 54
  average time/residue: 0.0539
  time to fit residues: 4.8521
Evaluate side-chains
  52 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 84 optimal weight:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0980
   chunk 35 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.119265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.099611 restraints weight = 11660.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.66
r_work: 0.3185 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7998  Z= 0.101
  Angle     :  0.515   9.647  10875  Z= 0.268
  Chirality :  0.044   0.236   1293
  Planarity :  0.003   0.023   1368
  Dihedral  :  6.061  55.630   1281
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.77 %
    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: -0.68 (0.27), residues: 999
  helix:  1.96 (0.34), residues: 258
  sheet: -0.18 (0.38), residues: 222
  loop : -1.93 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 252 
 TYR   0.016   0.001   TYR A 319 
 PHE   0.004   0.001   PHE B 256 
 TRP   0.002   0.000   TRP A  43 
 HIS   0.001   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7965)
  covalent geometry    : angle       0.50667 (10800)
  SS BOND              : bond        0.00559 (   24)
  SS BOND              : angle       1.27219 (   48)
  hydrogen bonds       : bond        0.02967 (  289)
  hydrogen bonds       : angle       4.58090 (  807)
  link_BETA1-4         : bond        0.00367 (    3)
  link_BETA1-4         : angle       1.19004 (    9)
  link_NAG-ASN         : bond        0.00224 (    6)
  link_NAG-ASN         : angle       1.14658 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  244 MET cc_start: 0.8895 (mtm) cc_final: 0.8590 (mtm)
  outliers start: 19
  outliers final: 14
  residues processed: 59
  average time/residue: 0.0526
  time to fit residues: 5.1071
Evaluate side-chains
  57 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0050
   chunk 49 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
A 426 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.117466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.097962 restraints weight = 11706.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.65
r_work: 0.3166 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7998  Z= 0.133
  Angle     :  0.544   9.690  10875  Z= 0.281
  Chirality :  0.045   0.238   1293
  Planarity :  0.003   0.024   1368
  Dihedral  :  6.053  55.001   1281
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.26 %
    Favored  : 85.68 %
  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: -0.69 (0.27), residues: 999
  helix:  2.43 (0.35), residues: 231
  sheet: -0.53 (0.33), residues: 279
  loop : -1.92 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 253 
 TYR   0.021   0.001   TYR B 319 
 PHE   0.005   0.001   PHE B 256 
 TRP   0.003   0.001   TRP A  43 
 HIS   0.002   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7965)
  covalent geometry    : angle       0.53515 (10800)
  SS BOND              : bond        0.00597 (   24)
  SS BOND              : angle       1.32961 (   48)
  hydrogen bonds       : bond        0.03205 (  289)
  hydrogen bonds       : angle       4.57308 (  807)
  link_BETA1-4         : bond        0.00415 (    3)
  link_BETA1-4         : angle       1.20060 (    9)
  link_NAG-ASN         : bond        0.00301 (    6)
  link_NAG-ASN         : angle       1.09925 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8978 (mtm) cc_final: 0.8665 (mtm)
  outliers start: 18
  outliers final: 18
  residues processed: 60
  average time/residue: 0.0491
  time to fit residues: 5.0146
Evaluate side-chains
  62 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  385 TYR
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0870
   chunk 97 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.118921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.099420 restraints weight = 11749.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.66
r_work: 0.3190 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7998  Z= 0.103
  Angle     :  0.518   9.652  10875  Z= 0.268
  Chirality :  0.044   0.235   1293
  Planarity :  0.003   0.023   1368
  Dihedral  :  6.005  55.171   1281
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.49 %
    Favored  : 85.22 %
  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: -0.65 (0.27), residues: 999
  helix:  2.00 (0.34), residues: 258
  sheet: -0.19 (0.35), residues: 249
  loop : -1.99 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 252 
 TYR   0.020   0.001   TYR B 319 
 PHE   0.004   0.001   PHE B 256 
 TRP   0.003   0.000   TRP A  43 
 HIS   0.001   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7965)
  covalent geometry    : angle       0.50999 (10800)
  SS BOND              : bond        0.00565 (   24)
  SS BOND              : angle       1.27734 (   48)
  hydrogen bonds       : bond        0.02883 (  289)
  hydrogen bonds       : angle       4.47131 (  807)
  link_BETA1-4         : bond        0.00455 (    3)
  link_BETA1-4         : angle       1.18204 (    9)
  link_NAG-ASN         : bond        0.00284 (    6)
  link_NAG-ASN         : angle       1.07039 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  244 MET cc_start: 0.8853 (mtm) cc_final: 0.8548 (mtm)
  outliers start: 20
  outliers final: 18
  residues processed: 63
  average time/residue: 0.0535
  time to fit residues: 5.5724
Evaluate side-chains
  60 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  385 TYR
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0770
   overall best weight:    0.8540

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.117602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.098151 restraints weight = 11720.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.64
r_work: 0.3166 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7998  Z= 0.129
  Angle     :  0.534   9.707  10875  Z= 0.276
  Chirality :  0.044   0.238   1293
  Planarity :  0.003   0.024   1368
  Dihedral  :  6.022  55.098   1281
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.37 %
    Favored  : 85.11 %
  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: -0.69 (0.27), residues: 999
  helix:  1.99 (0.34), residues: 258
  sheet: -0.14 (0.35), residues: 243
  loop : -2.05 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 253 
 TYR   0.028   0.001   TYR A 319 
 PHE   0.005   0.001   PHE B 256 
 TRP   0.003   0.001   TRP A  43 
 HIS   0.002   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7965)
  covalent geometry    : angle       0.52533 (10800)
  SS BOND              : bond        0.00587 (   24)
  SS BOND              : angle       1.30520 (   48)
  hydrogen bonds       : bond        0.03074 (  289)
  hydrogen bonds       : angle       4.49969 (  807)
  link_BETA1-4         : bond        0.00463 (    3)
  link_BETA1-4         : angle       1.19569 (    9)
  link_NAG-ASN         : bond        0.00277 (    6)
  link_NAG-ASN         : angle       1.12504 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8956 (mtm) cc_final: 0.8647 (mtm)
  outliers start: 22
  outliers final: 20
  residues processed: 63
  average time/residue: 0.0486
  time to fit residues: 5.0887
Evaluate side-chains
  64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  385 TYR
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.119126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.098954 restraints weight = 11793.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.72
r_work: 0.3159 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7998  Z= 0.130
  Angle     :  0.540   9.706  10875  Z= 0.280
  Chirality :  0.045   0.236   1293
  Planarity :  0.003   0.024   1368
  Dihedral  :  6.046  55.115   1281
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.26 %
    Favored  : 84.99 %
  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: -0.60 (0.27), residues: 999
  helix:  2.48 (0.35), residues: 231
  sheet: -0.32 (0.32), residues: 288
  loop : -1.99 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 253 
 TYR   0.019   0.001   TYR B 319 
 PHE   0.005   0.001   PHE B 256 
 TRP   0.003   0.001   TRP A  43 
 HIS   0.002   0.000   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7965)
  covalent geometry    : angle       0.53227 (10800)
  SS BOND              : bond        0.00591 (   24)
  SS BOND              : angle       1.28762 (   48)
  hydrogen bonds       : bond        0.03064 (  289)
  hydrogen bonds       : angle       4.47081 (  807)
  link_BETA1-4         : bond        0.00465 (    3)
  link_BETA1-4         : angle       1.19866 (    9)
  link_NAG-ASN         : bond        0.00274 (    6)
  link_NAG-ASN         : angle       1.12912 (   18)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8913 (mtm) cc_final: 0.8603 (mtm)
  outliers start: 24
  outliers final: 20
  residues processed: 64
  average time/residue: 0.0500
  time to fit residues: 5.3119
Evaluate side-chains
  63 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain C residue   26 GLU
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  385 TYR
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.115645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.096192 restraints weight = 11732.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.63
r_work: 0.3137 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7998  Z= 0.173
  Angle     :  0.583   9.783  10875  Z= 0.301
  Chirality :  0.046   0.238   1293
  Planarity :  0.003   0.026   1368
  Dihedral  :  6.143  54.980   1281
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.37 %
    Favored  : 85.11 %
  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: -0.76 (0.27), residues: 999
  helix:  2.40 (0.35), residues: 231
  sheet: -0.73 (0.31), residues: 303
  loop : -1.91 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 253 
 TYR   0.020   0.001   TYR B 319 
 PHE   0.005   0.001   PHE C 207 
 TRP   0.003   0.001   TRP A 284 
 HIS   0.002   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7965)
  covalent geometry    : angle       0.57414 (10800)
  SS BOND              : bond        0.00638 (   24)
  SS BOND              : angle       1.39808 (   48)
  hydrogen bonds       : bond        0.03370 (  289)
  hydrogen bonds       : angle       4.55694 (  807)
  link_BETA1-4         : bond        0.00429 (    3)
  link_BETA1-4         : angle       1.24195 (    9)
  link_NAG-ASN         : bond        0.00250 (    6)
  link_NAG-ASN         : angle       1.18792 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1473.71 seconds
wall clock time: 26 minutes 2.56 seconds (1562.56 seconds total)